X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.31 α = 90
b = 125.47 β = 90
c = 33.88 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 bent Si-mirror 2003-04-15
Diffraction Radiation
Monochromator Protocol
bent Ge(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 0.9000 APS 14-BM-C

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
1.1 28.7 91.0 0.077 0.089 -- 3.8 62884 62884 0.0 0.0 8.4
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)
1.1 1.14 81.2 0.27 0.27 1.0 3.1 5509

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
FOURIER SYNTHESIS 1.1 28.64 -- 0.0 62884 58988 3164 89.94 0.1547 0.1547 0.1536 0.177 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 1.1 1.129 3708 208 3708 0.213 0.231 -- 77.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 10.562
Anisotropic B[1][1] 0.56
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.43
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.13
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 3.184
r_symmetry_vdw_other 0.243
r_bond_other_d 0.002
r_angle_other_deg 2.021
r_gen_planes_other 0.001
r_symmetry_vdw_refined 0.191
r_symmetry_hbond_refined 0.191
r_mcbond_it 1.871
r_sphericity_free 6.979
r_bond_refined_d 0.022
r_sphericity_bonded 4.297
r_angle_refined_deg 1.936
r_nbd_other 0.266
r_gen_planes_refined 0.012
r_nbd_refined 0.215
r_xyhbond_nbd_refined 0.152
r_rigid_bond_restr 1.945
r_nbtor_other 0.103
r_chiral_restr 0.157
r_scangle_it 4.479
r_dihedral_angle_1_deg 6.982
r_mcangle_it 2.611
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.035
Luzzati Sigma A (Observed) 0.024
Luzzati ESD (R-Free Set) 0.035
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1419
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 244

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.22
XDISPLAYF data reduction
d*TREK data scaling