X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.5
Temperature 291.0
Details 0.4 M (NH4)2SO4, 0.05 M MES-NaOH pH 6.5, vapor diffusion, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.13 α = 90
b = 93.14 β = 90
c = 106.1 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 315r -- 2009-07-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 1.0000 ESRF ID29

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
2.89 46.1 96.9 0.078 0.078 -- 3.7 15101 15101 0.0 0.0 --
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)
3.0 3.16 97.8 0.453 0.453 1.7 3.8 2192

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
MOLECULAR REPLACEMENT 3.0 20.0 -- 0.0 14794 14233 777 96.21 0.2218 0.2218 0.2184 0.2854 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 3.0 3.076 -- 56 1026 0.281 0.321 -- 96.78
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.6742
Anisotropic B[1][1] -2.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.46
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.45
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.007
r_xyhbond_nbd_refined 0.149
r_symmetry_vdw_refined 0.186
r_nbtor_refined 0.305
r_scangle_it 1.251
r_scbond_it 0.725
r_angle_refined_deg 1.084
r_chiral_restr 0.069
r_dihedral_angle_3_deg 19.8
r_dihedral_angle_4_deg 19.056
r_mcangle_it 0.716
r_dihedral_angle_1_deg 5.194
r_nbd_refined 0.206
r_symmetry_hbond_refined 0.136
r_gen_planes_refined 0.003
r_dihedral_angle_2_deg 35.826
r_mcbond_it 0.389
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4296
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 23

Software

Software
Software Name Purpose
SCALA data scaling version: 3.2.25
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
XDS data scaling
XDS data reduction