X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details 25% PEG3350, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.6 α = 90
b = 98.35 β = 90
c = 99.36 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
XDSdataset 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2011-07-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97911 APS 19-ID

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
1.85 49.18 99.96 0.12 -- -- 7.11 18676 18636 -- -- --
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)
1.85 1.95 99.97 0.88 -- -- 7.13 2689

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 1.85 39.86 -- 0.0 -- 18636 935 99.86 -- 0.1883 0.1866 0.2215 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 1.85 1.898 -- 64 1294 0.376 0.461 -- 99.926
X Ray Diffraction 1.898 1.95 -- 74 1249 0.277 0.325 -- 99.924
X Ray Diffraction 1.95 2.006 -- 67 1214 0.194 0.271 -- 99.922
X Ray Diffraction 2.006 2.068 -- 73 1176 0.179 0.237 -- 100.0
X Ray Diffraction 2.068 2.136 -- 62 1145 0.16 0.184 -- 100.0
X Ray Diffraction 2.136 2.21 -- 57 1122 0.166 0.23 -- 99.915
X Ray Diffraction 2.21 2.293 -- 53 1085 0.18 0.192 -- 99.912
X Ray Diffraction 2.293 2.387 -- 49 1037 0.173 0.193 -- 100.0
X Ray Diffraction 2.387 2.492 -- 48 1010 0.18 0.193 -- 99.906
X Ray Diffraction 2.492 2.614 -- 52 945 0.167 0.274 -- 100.0
X Ray Diffraction 2.614 2.754 -- 59 915 0.173 0.219 -- 99.795
X Ray Diffraction 2.754 2.921 -- 37 876 0.189 0.188 -- 100.0
X Ray Diffraction 2.921 3.121 -- 49 811 0.181 0.212 -- 99.884
X Ray Diffraction 3.121 3.369 -- 37 772 0.194 0.239 -- 99.753
X Ray Diffraction 3.369 3.688 -- 42 692 0.18 0.22 -- 100.0
X Ray Diffraction 3.688 4.119 -- 35 648 0.158 0.17 -- 99.708
X Ray Diffraction 4.119 4.748 -- 21 577 0.147 0.189 -- 99.833
X Ray Diffraction 4.748 5.795 -- 32 488 0.184 0.187 -- 99.617
X Ray Diffraction 5.795 8.109 -- 15 400 0.226 0.191 -- 99.045
X Ray Diffraction 8.109 39.858 -- 9 245 0.223 0.273 -- 97.318
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.7861
Anisotropic B[1][1] 0.69
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.88
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.19
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 0.81
r_angle_other_deg 1.013
r_bond_refined_d 0.017
r_scbond_it 2.278
r_dihedral_angle_2_deg 35.704
r_scangle_it 3.632
r_gen_planes_other 0.001
r_mcbond_other 0.256
r_angle_refined_deg 1.476
r_dihedral_angle_3_deg 11.902
r_gen_planes_refined 0.007
r_chiral_restr 0.102
r_dihedral_angle_1_deg 5.493
r_bond_other_d 0.001
r_mcangle_it 1.401
r_dihedral_angle_4_deg 15.545
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1360
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 117

Software

Software
Software Name Purpose
SCALA data scaling version: CCP4_3.3.16
PHASER phasing
REFMAC refinement version: refmac_5.5.0109
PDB_EXTRACT data extraction version: 3.11
XDS data reduction