X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 25.0
Details Protein Solution: 0.16 mM protein, 0.5 M KCl, 50 mM Tris Cl (pH 7.5), 1 mM DTT, 10% glycerol, 1 mM IMP Well Solution: 2.2 M ammonium sulfate, PEG 550 MME, 0.1 M Tris Cl (pH 7.5), 10% glycerol, 0.01 mM beta-mercaptoethanol IMP does not bind in crystal due to excess ammonium sulfate. Crystallization is reproducible in the absence of IMP. , VAPOR DIFFUSION, HANGING DROP, temperature 25K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 123.28 α = 90
b = 123.28 β = 90
c = 130.11 γ = 90
Symmetry
Space Group I 4

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1997-05-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12B -- NSLS X12B

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
2.2 100 99.6 0.131 -- -- 6.8 255126 36820 0.0 0.0 27.5
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)
2.4 2.5 95.8 0.343 -- -- 3.4 3620

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
-- 2.4 8.0 0.0 0.0 36820 36820 3732 99.6 -- 0.214 0.214 0.262 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 2.4 2.55 -- 600 5428 0.274 0.329 0.013 98.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model GROUP
Mean Isotropic B 35.2
Anisotropic B[1][1] -4.84
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.84
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 9.68
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 23.5
c_bond_d 0.007
c_angle_deg 1.4
c_improper_angle_d 0.82
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.29
Luzzati Sigma A (Observed) 0.3
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.36
Luzzati Sigma A (R-Free Set) 0.37
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4564
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 107

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement
DENZO data reduction
SCALEPACK data scaling