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 = 58.17 α = 90
b = 58.17 β = 90
c = 391.82 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 -- 2010-09-30
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
2.01 65.3 97.8 0.08 -- -- 5.6 -- 27252 -- -- --
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)
2.01 2.04 98.7 0.346 -- -- 4.8 1281

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 2.01 39.889 -- 0.0 -- 27229 1370 98.16 -- 0.2053 0.202 0.266 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 2.01 2.061 -- 101 1813 0.31 0.36 -- 97.8
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.1704
Anisotropic B[1][1] 0.59
Anisotropic B[1][2] 0.3
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.59
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.89
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.505
r_scbond_it 3.086
r_mcangle_it 1.705
r_mcbond_it 0.988
r_gen_planes_refined 0.009
r_chiral_restr 0.13
r_dihedral_angle_4_deg 17.004
r_dihedral_angle_3_deg 15.742
r_dihedral_angle_2_deg 38.024
r_dihedral_angle_1_deg 5.498
r_angle_refined_deg 1.861
r_bond_refined_d 0.02
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2882
Nucleic Acid Atoms 0
Heterogen Atoms 49
Solvent Atoms 245

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