X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 297.0
Details Sodium MES, Sodium citrate, MEthyl Ether PEG 5000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.47 α = 90
b = 55.47 β = 90
c = 57.67 γ = 120
Symmetry
Space Group P 62

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) 2003-06-26
Diffraction Radiation
Monochromator Protocol
Diamond (111) double-crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-ID-B 0.979 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
1.9 20 98.3 0.042 -- -- 10.1 -- 7570 -- 2.0 21.2
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)
1.9 1.97 75.2 0.303 -- 2.06 2.9 598

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
MAD 1.9 20.0 0.0 0.0 7209 7209 369 94.76 0.18469 0.18469 0.18217 0.2323 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 1.9 1.95 598 27 342 0.258 0.267 -- 75.2
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.214
Anisotropic B[1][1] -0.13
Anisotropic B[1][2] -0.07
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.13
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.2
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.01
r_gen_planes_other 0.01
r_symmetry_hbond_refined 0.164
r_scangle_it 4.482
r_bond_refined_d 0.02
r_xyhbond_nbd_refined 0.187
r_symmetry_vdw_other 0.276
r_dihedral_angle_1_deg 6.185
r_mcangle_it 1.851
r_angle_other_deg 1.025
r_bond_other_d 0.002
r_nbd_other 0.244
r_angle_refined_deg 1.861
r_mcbond_it 1.058
r_chiral_restr 0.338
r_nbd_refined 0.216
r_nbtor_other 0.091
r_symmetry_vdw_refined 0.233
r_scbond_it 2.796
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 818
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 109

Software

Software
Software Name Purpose
MAR data collection
SCALEPACK data scaling
SOLVE phasing version: RESOLVE
REFMAC refinement version: 5.1.24
MAR data reduction
RESOLVE phasing