X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 297.0
Details Glycine, MEPEG 5000, triethanolamine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.11 α = 90
b = 85.07 β = 90
c = 121.82 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH Bent cylindrical Si-mirror (Rh coating) 2003-06-20
Diffraction Radiation
Monochromator Protocol
Diamond (111) double-crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-ID-B 0.9790 APS 14-ID-B

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 25 90.5 0.133 0.133 -- 6.09 55478 50628 -- -3.0 23.3
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)
2.0 2.07 43.6 0.687 0.687 1.11 0.39 2384

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 2.0 24.92 0.0 0.0 55478 48056 2572 91.26 0.18884 0.1888 0.18635 0.23588 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 2.0 2.07 2384 86 1541 0.297 0.353 -- 44.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.896
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.836
r_gen_planes_refined 0.01
r_symmetry_vdw_refined 0.158
r_gen_planes_other 0.011
r_nbd_refined 0.211
r_bond_refined_d 0.02
r_bond_other_d 0.003
r_xyhbond_nbd_refined 0.168
r_chiral_restr 0.103
r_symmetry_vdw_other 0.243
r_symmetry_hbond_refined 0.211
r_angle_other_deg 0.887
r_nbd_other 0.259
r_angle_refined_deg 1.636
r_dihedral_angle_1_deg 6.773
r_mcangle_it 1.615
r_nbtor_other 0.093
r_mcbond_it 0.92
r_scbond_it 2.443
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5634
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 410

Software

Software
Software Name Purpose
MAR345 data collection
SCALEPACK data scaling
SOMORE model building
REFMAC refinement version: 5.1.24
SOMORE phasing