X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 277.0
Details 20% PEG 3350, 0.2M Magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.5 α = 99.04
b = 60.33 β = 100.37
c = 78.81 γ = 105.08
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2009-06-15
Diffraction Radiation
Monochromator Protocol
Double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9794 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
2.09 50 98.0 0.068 -- -- 2.6 -- 47621 -- -- --
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)
2.1 2.18 97.3 0.241 -- -- 2.6 4765

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
-- 2.09 28.45 -- 0.0 -- 47599 2416 97.46 -- 0.197 0.195 0.236 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 2.093 2.147 -- 166 3067 0.229 0.303 -- 89.656
X Ray Diffraction 2.147 2.206 -- 158 3248 0.217 0.27 -- 97.231
X Ray Diffraction 2.206 2.269 -- 175 3153 0.233 0.262 -- 97.31
X Ray Diffraction 2.269 2.339 -- 173 3046 0.234 0.308 -- 97.368
X Ray Diffraction 2.339 2.415 -- 173 2990 0.224 0.289 -- 97.714
X Ray Diffraction 2.415 2.499 -- 149 2845 0.227 0.287 -- 97.715
X Ray Diffraction 2.499 2.593 -- 154 2783 0.239 0.301 -- 97.998
X Ray Diffraction 2.593 2.698 -- 125 2744 0.216 0.249 -- 98.22
X Ray Diffraction 2.698 2.816 -- 124 2560 0.22 0.279 -- 98.064
X Ray Diffraction 2.816 2.952 -- 130 2482 0.213 0.263 -- 98.232
X Ray Diffraction 2.952 3.11 -- 140 2312 0.2 0.267 -- 98.632
X Ray Diffraction 3.11 3.296 -- 98 2269 0.193 0.245 -- 98.666
X Ray Diffraction 3.296 3.521 -- 116 2105 0.187 0.223 -- 98.887
X Ray Diffraction 3.521 3.798 -- 102 1981 0.182 0.203 -- 99.002
X Ray Diffraction 3.798 4.153 -- 109 1798 0.16 0.181 -- 99.116
X Ray Diffraction 4.153 4.631 -- 83 1643 0.146 0.17 -- 99.138
X Ray Diffraction 4.631 5.324 -- 80 1455 0.15 0.18 -- 99.288
X Ray Diffraction 5.324 6.464 -- 75 1217 0.214 0.266 -- 99.461
X Ray Diffraction 6.464 8.914 -- 61 963 0.199 0.243 -- 99.129
X Ray Diffraction 8.914 28.449 -- 25 522 0.212 0.21 -- 89.088
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.225
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.15
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.13
Anisotropic B[3][3] 0.11
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 16.617
r_bond_refined_d 0.012
r_mcangle_it 0.866
r_dihedral_angle_3_deg 16.621
r_mcbond_it 0.48
r_scbond_it 1.547
r_angle_refined_deg 1.343
r_dihedral_angle_1_deg 6.102
r_gen_planes_refined 0.005
r_scangle_it 2.305
r_dihedral_angle_2_deg 40.11
r_chiral_restr 0.09
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5992
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 258

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: refmac_5.5.0102
PDB_EXTRACT data extraction version: 3.004
SBC-Collect data collection
HKL-3000 data reduction
SHELX phasing
MLPHARE phasing
DM phasing
ARP/wARP model building
Coot model building