X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 277.0
Details Inhibitor soaked into crystal generated according to Kim et al. (1996) Cell, 87, 343-355, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 225.45 α = 90
b = 225.45 β = 90
c = 75.89 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC MIRRORS --
Diffraction Radiation
Monochromator Protocol
YALE MIRRORS + Ni FILTER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200H 1.5418 -- --

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
2.6 40 96.3 0.052 -- -- -- 22723 21878 -- 1.0 --
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)
2.6 2.69 92.0 0.238 -- 4.5 -- 2074

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 2.6 20.0 -- 1.0 20724 20724 1115 100.0 0.18508 0.18508 0.18318 0.2195 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 2.6 2.667 -- 72 1441 0.266 0.36 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.569
Anisotropic B[1][1] -1.0
Anisotropic B[1][2] -0.5
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.51
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 8.583
r_bond_refined_d 0.016
r_angle_refined_deg 1.741
r_dihedral_angle_1_deg 6.551
r_chiral_restr 0.11
r_gen_planes_refined 0.006
r_nbd_refined 0.237
r_xyhbond_nbd_refined 0.173
r_symmetry_vdw_refined 0.256
r_symmetry_hbond_refined 0.232
r_mcbond_it 1.632
r_mcangle_it 3.305
r_scbond_it 5.492
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2732
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 107

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (TRUNCATE) Data Reduction (data scaling)
REFMAC Structure Refinement
Software
Software Name Purpose
REFMAC refinement
REFMAC model building
TRUNCATE data reduction
DENZO data collection