X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.8
Temperature 293.0
Details 26% PEG 300, 0.1 M sodium acetate, 2mM phosphoglycolohydroxamate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.8 α = 90
b = 119.61 β = 90
c = 164.1 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2009-06-02
Diffraction Radiation
Monochromator Protocol
Si 220 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID

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
1.58 93.9 94.0 -- -- -- -- 79039 78320 -- -- --
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)
1.58 1.64 77.5 0.279 -- 4.2 -- --

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 1.58 49.74 -- 0.0 79039 78207 3910 93.9 -- 0.1893 0.1885 0.2054 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 1.58 1.622 -- 227 4359 0.266 0.278 -- 76.26
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.0601
Anisotropic B[1][1] 2.52
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.55
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.97
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 36.994
r_chiral_restr 0.094
r_gen_planes_refined 0.005
r_mcbond_it 0.564
r_dihedral_angle_1_deg 18.029
r_metal_ion_refined 0.473
r_scbond_it 1.699
r_bond_refined_d 0.01
r_nbd_refined 0.211
r_nbtor_refined 0.302
r_angle_refined_deg 1.194
r_dihedral_angle_4_deg 18.847
r_xyhbond_nbd_refined 0.112
r_dihedral_angle_3_deg 12.342
r_symmetry_metal_ion_refined 0.027
r_symmetry_vdw_refined 0.198
r_symmetry_hbond_refined 0.143
r_scangle_it 2.835
r_mcangle_it 1.018
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2583
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 513

Software

Software
Software Name Purpose
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling