X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.8
Temperature 292.0
Details PEG 6000, KCl, NH4Cl, MGCl2, KAcetate, pH 5.8, vapor diffusion, sitting drop, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 211.74 α = 90
b = 299.52 β = 90
c = 573.59 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror 2005-11-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.02 NSLS X29A

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.85 50 99.9 0.163 -- -- 7.0 -- 422741 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.85 2.92 98.5 -- -- -- 4.9 29680

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.9 49.7 1.04 0.0 422741 397264 3880 99.9 -- -- 0.193 0.238 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.9 2.92 7779 77 7702 0.399 0.435 -- --
X Ray Diffraction 2.92 2.94 7891 77 7814 0.358 0.417 -- --
X Ray Diffraction 2.94 2.96 7904 71 7833 0.345 0.386 -- --
X Ray Diffraction 2.96 2.98 7862 86 7776 0.324 0.33 -- --
X Ray Diffraction 2.98 3.0 7918 74 7844 0.315 0.373 -- --
X Ray Diffraction 3.0 3.03 7897 74 7823 0.306 0.38 -- --
X Ray Diffraction 3.03 3.05 7935 78 7857 0.293 0.406 -- --
X Ray Diffraction 3.05 3.07 7825 87 7738 0.276 0.319 -- --
X Ray Diffraction 3.07 3.1 7920 74 7846 0.264 0.358 -- --
X Ray Diffraction 3.1 3.12 7911 76 7835 0.249 0.267 -- --
X Ray Diffraction 3.12 3.15 7939 71 7868 0.249 0.312 -- --
X Ray Diffraction 3.15 3.18 7854 71 7783 0.218 0.262 -- --
X Ray Diffraction 3.18 3.21 7925 94 7831 0.226 0.282 -- --
X Ray Diffraction 3.21 3.24 7872 76 7796 0.226 0.312 -- --
X Ray Diffraction 3.24 3.27 7970 80 7890 0.211 0.258 -- --
X Ray Diffraction 3.27 3.3 7866 76 7790 0.218 0.286 -- --
X Ray Diffraction 3.3 3.33 7963 54 7909 0.221 0.274 -- --
X Ray Diffraction 3.33 3.37 7882 76 7806 0.214 0.273 -- --
X Ray Diffraction 3.37 3.4 7936 81 7855 0.205 0.249 -- --
X Ray Diffraction 3.4 3.44 7910 83 7827 0.208 0.236 -- --
X Ray Diffraction 3.44 3.48 7899 66 7833 0.195 0.232 -- --
X Ray Diffraction 3.48 3.52 7976 74 7902 0.196 0.237 -- --
X Ray Diffraction 3.52 3.56 7868 77 7791 0.197 0.241 -- --
X Ray Diffraction 3.56 3.61 7922 63 7859 0.197 0.304 -- --
X Ray Diffraction 3.61 3.65 7975 84 7891 0.185 0.254 -- --
X Ray Diffraction 3.65 3.7 7858 79 7779 0.18 0.215 -- --
X Ray Diffraction 3.7 3.76 7934 79 7855 0.169 0.229 -- --
X Ray Diffraction 3.76 3.81 7980 80 7900 0.169 0.204 -- --
X Ray Diffraction 3.81 3.87 7934 67 7867 0.176 0.262 -- --
X Ray Diffraction 3.87 3.94 7924 82 7842 0.178 0.259 -- --
X Ray Diffraction 3.94 4.0 7924 74 7850 0.159 0.232 -- --
X Ray Diffraction 4.0 4.08 7974 81 7893 0.164 0.199 -- --
X Ray Diffraction 4.08 4.15 7932 87 7845 0.166 0.213 -- --
X Ray Diffraction 4.15 4.24 7924 78 7846 0.149 0.202 -- --
X Ray Diffraction 4.24 4.33 7949 83 7866 0.145 0.202 -- --
X Ray Diffraction 4.33 4.43 7952 84 7868 0.156 0.197 -- --
X Ray Diffraction 4.43 4.54 7921 64 7857 0.149 0.212 -- --
X Ray Diffraction 4.54 4.67 7996 90 7906 0.154 0.165 -- --
X Ray Diffraction 4.67 4.8 7967 77 7890 0.15 0.199 -- --
X Ray Diffraction 4.8 4.96 7971 75 7896 0.145 0.179 -- --
X Ray Diffraction 4.96 5.13 7951 89 7862 0.149 0.167 -- --
X Ray Diffraction 5.13 5.34 7979 80 7899 0.154 0.221 -- --
X Ray Diffraction 5.34 5.58 8004 75 7929 0.155 0.22 -- --
X Ray Diffraction 5.58 5.88 8026 71 7955 0.163 0.212 -- --
X Ray Diffraction 5.88 6.24 8002 83 7919 0.174 0.227 -- --
X Ray Diffraction 6.24 6.73 8007 69 7938 0.171 0.205 -- --
X Ray Diffraction 6.73 7.4 8044 79 7965 0.165 0.22 -- --
X Ray Diffraction 7.4 8.47 8101 97 8004 0.186 0.216 -- --
X Ray Diffraction 8.47 10.65 8127 79 8048 0.201 0.212 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 58.2
Anisotropic B[1][1] 2.95
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.65
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.31
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.34
c_scbond_it 0.84
c_angle_deg 1.0
c_dihedral_angle_d 15.9
c_mcangle_it 1.34
c_mcbond_it 0.74
c_scangle_it 1.34
c_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Sigma A (Observed) 0.47
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.39
Luzzati Sigma A (R-Free Set) 0.57
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 29364
Nucleic Acid Atoms 61621
Heterogen Atoms 274
Solvent Atoms 7784

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement
PDB_EXTRACT data extraction version: 2.000
CBASS data collection
HKL-2000 data reduction
HKL-2000 data scaling
CNS phasing