X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 303.0
Details 0.1 M phosphate citrate pH 5.5, 0.15M sodium sulfate, 0.01M MgCl2, 1 M guanidium hydrochloride, 28% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.64 α = 90
b = 80.11 β = 90
c = 137.22 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2008-07-24
CCD RAYONIX MX-225 beryllium lenses 2008-07-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
silicon SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 0.97915 APS 21-ID-D
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97872 APS 21-ID-G

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
1.4 28.9 98.8 0.048 0.045 -- 8.5 138158 136662 -- -- --
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)
1.4 1.46 95.5 0.405 0.379 5.3 7.9 --

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
SAD 1.4 28.9 -- -- 136662 129802 6859 98.68 -- 0.16587 0.16491 0.18424 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 1.4 1.436 -- 487 8967 0.193 0.221 -- 93.51
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.181
Anisotropic B[1][1] 0.52
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.32
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.2
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.181
r_scbond_it 1.651
r_mcangle_it 0.892
r_mcbond_other 0.175
r_mcbond_it 0.778
r_nbd_refined 0.225
r_gen_planes_other 0.003
r_gen_planes_refined 0.006
r_chiral_restr 0.072
r_dihedral_angle_4_deg 18.476
r_dihedral_angle_3_deg 12.794
r_dihedral_angle_2_deg 32.878
r_dihedral_angle_1_deg 4.709
r_angle_other_deg 0.901
r_angle_refined_deg 1.195
r_bond_other_d 0.002
r_bond_refined_d 0.009
r_nbd_other 0.202
r_nbtor_refined 0.177
r_nbtor_other 0.082
r_xyhbond_nbd_refined 0.138
r_symmetry_vdw_refined 0.266
r_symmetry_vdw_other 0.242
r_symmetry_hbond_refined 0.146
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6056
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 573

Software

Computing
Computing Package Purpose
MD2-microdiffractometer Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
SHARP Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
SHARP model building
MD2-microdiffractometer data collection