X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.7
Temperature 294.0
Details 28% PEG 8000, 0.2 M (NH4)2SO4, 0.1 M sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 111.03 α = 90
b = 111.03 β = 90
c = 113.43 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2004-01-07
CCD ADSC QUANTUM 315 -- 2004-06-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.00000 NSLS X25
SYNCHROTRON NSLS BEAMLINE X12C 0.97791 NSLS X12C

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
2.2 30 93.9 -- -- -- -- -- 34399 2.0 2.0 --
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)
2.2 2.26 73.9 -- -- -- -- --

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 2.2 79.81 -- 2.0 -- 32633 1703 93.83 -- 0.20527 0.20251 0.25832 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 2.2 2.257 -- 88 1834 0.254 0.283 -- 72.12
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.438
Anisotropic B[1][1] -1.79
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.79
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.58
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 2.585
r_scbond_it 3.555
r_xyhbond_nbd_refined 0.208
r_dihedral_angle_2_deg 38.091
r_mcbond_it 1.596
r_chiral_restr 0.179
r_gen_planes_refined 0.01
r_symmetry_vdw_refined 0.243
r_dihedral_angle_3_deg 18.771
r_symmetry_hbond_refined 0.24
r_scangle_it 5.441
r_nbd_refined 0.239
r_angle_refined_deg 2.105
r_dihedral_angle_1_deg 14.682
r_nbtor_refined 0.311
r_bond_refined_d 0.025
r_dihedral_angle_4_deg 21.4
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2935
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 274

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
ADSC data collection
HKL-2000 data scaling
SOLVE phasing