X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 303.0
Details 0.1 M phosphate-citrate pH 5, 0.2 M NaCl, 16% PEG 8000, 1M Guanidium hydrochloride, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.09 α = 90
b = 70.09 β = 90
c = 349.63 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2008-04-23
CCD RAYONIX MX-225 beryllium lenses 2008-04-23
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
2.6 29.5 99.9 0.079 0.074 -- 8.1 28160 28151 -- -- 42.1
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)
2.6 2.72 100.0 0.572 0.522 3.2 6.0 3331

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 2.6 29.14 -- -- 28151 26710 1438 99.96 0.24371 0.24371 0.24132 0.28883 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 2.6 2.667 1897 93 1897 0.366 0.451 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 55.918
Anisotropic B[1][1] 2.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.04
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.464
r_scbond_it 0.968
r_mcangle_it 0.58
r_mcbond_other 0.086
r_mcbond_it 0.522
r_symmetry_hbond_refined 0.16
r_symmetry_vdw_other 0.263
r_symmetry_vdw_refined 0.202
r_xyhbond_nbd_refined 0.15
r_nbtor_other 0.085
r_nbtor_refined 0.179
r_nbd_other 0.185
r_bond_refined_d 0.011
r_bond_other_d 0.002
r_angle_refined_deg 1.203
r_angle_other_deg 0.89
r_dihedral_angle_1_deg 5.538
r_dihedral_angle_2_deg 34.326
r_dihedral_angle_3_deg 17.444
r_dihedral_angle_4_deg 18.828
r_chiral_restr 0.067
r_gen_planes_refined 0.003
r_gen_planes_other 0.001
r_nbd_refined 0.226
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5967
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 30

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