X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Nanovolume
pH 8.1
Temperature 277.0
Details PEG 4000, glycerol, magnesium chloride, Tris, pH 8.1, nanovolume, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 91.52 α = 90
b = 92.27 β = 90
c = 118.17 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-07-31
Diffraction Radiation
Monochromator Protocol
Si crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.3 1.0 ALS 5.0.3

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
1.85 25 90.0 0.064 -- -- 4.45 86600 77944 2.0 2.0 13.3
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)
1.85 1.89 93.0 0.45 -- 3.0 4.5 5314

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 1.85 25.0 0.0 0.0 73241 73241 3868 89.79 0.17135 0.17135 0.16938 0.20836 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 1.85 1.898 -- 269 5507 0.198 0.249 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 13.859
Anisotropic B[1][1] 2.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.65
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.43
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.164
r_bond_refined_d 0.008
r_angle_refined_deg 1.112
r_symmetry_vdw_refined 0.177
r_mcbond_it 0.443
r_scangle_it 2.96
r_scbond_it 1.879
r_gen_planes_refined 0.004
r_dihedral_angle_1_deg 5.523
r_chiral_restr 0.075
r_xyhbond_nbd_refined 0.119
r_nbd_refined 0.194
r_mcangle_it 0.885
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7115
Nucleic Acid Atoms 0
Heterogen Atoms 92
Solvent Atoms 700

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.19
HKL-2000 data reduction
SCALEPACK data scaling
SHELXS phasing