X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 291.0
Details 12.5 mg/mL protein in 250 uM inhibitor, 250 uM IPP, 1 mM magnesium chloride, mother liquor: 100 mM sodium acetate, pH 4.6-5.2, 200 mM ammonium sulfate, 2-10% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.87 α = 90
b = 57.87 β = 90
c = 392.44 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2011-02-02
Diffraction Radiation
Monochromator Protocol
Si(111) channel cut SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X6A 0.979 NSLS X6A

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
2.1 65.41 93.2 0.113 -- -- 7.6 -- 22705 -- -- --
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)
2.1 2.14 98.2 0.509 -- -- 6.7 1158

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
FOURIER SYNTHESIS 2.1 19.891 -- 0.0 -- 22545 1156 92.82 -- 0.221 0.2178 0.2789 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 2.1 2.152 -- 81 1583 0.24 0.305 -- 96.74
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.5472
Anisotropic B[1][1] 1.89
Anisotropic B[1][2] 0.94
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.89
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.83
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.319
r_scbond_it 3.0
r_mcangle_it 1.678
r_mcbond_it 1.0
r_gen_planes_refined 0.008
r_chiral_restr 0.113
r_dihedral_angle_4_deg 19.269
r_dihedral_angle_3_deg 17.712
r_dihedral_angle_2_deg 39.759
r_dihedral_angle_1_deg 6.003
r_angle_refined_deg 1.778
r_bond_refined_d 0.021
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2882
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 89

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
REFMAC Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
SCALEPACK data reduction