X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details 1 mM EDTA, 10 mM sodium phosphate, 0.35-0.50 M ammonium sulfate - crystals were soaked with the inhibitor, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.22 α = 90
b = 85.08 β = 90
c = 64.4 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD CCD-PXL-L600 -- 2003-04-07
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 1.541 -- --

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
1.7 51.3 99.94 0.07 0.07 -- -- 25485 25485 0.0 0.0 --

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 1.7 51.3 0.0 0.0 25486 25485 1350 99.94 0.20985 0.20985 0.2083 0.23845 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 1.7 1.744 -- 90 1860 0.22 0.285 -- 99.49
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.4
Anisotropic B[1][1] -0.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.13
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.657
r_scbond_it 3.298
r_mcangle_it 2.147
r_mcbond_other 0.311
r_mcbond_it 2.215
r_symmetry_hbond_refined 0.238
r_symmetry_vdw_other 0.302
r_symmetry_vdw_refined 0.335
r_xyhbond_nbd_refined 0.225
r_nbtor_other 0.088
r_nbtor_refined 0.184
r_nbd_other 0.207
r_bond_refined_d 0.022
r_bond_other_d 0.008
r_angle_refined_deg 2.361
r_angle_other_deg 0.961
r_dihedral_angle_1_deg 6.933
r_dihedral_angle_2_deg 36.24
r_dihedral_angle_3_deg 15.762
r_dihedral_angle_4_deg 14.526
r_chiral_restr 0.094
r_gen_planes_refined 0.031
r_gen_planes_other 0.059
r_nbd_refined 0.201
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1752
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 217

Software

Computing
Computing Package Purpose
R-AXIS Data Reduction (intensity integration)
R-AXIS Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement