X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.25
Temperature 298.0
Details 15% Peg 6000, 0.2 M Magnesium acetate, 0.1M Tris-HCl. Protein buffer 0.2M MgCl2, 0.5 mM EDTA , 0.5 mM DTT, 2mM Tris-HCl pH7.2. 0.2 M MgCl2 was necessary to make protein monodisperse. Protein:precipitant ratio 1:1. Plate like crystals (0.08 mm X 0.2 mm X 0.2 mm)Crystals grew in two to three weeks, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.43 α = 90
b = 108.43 β = 90
c = 152.88 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Mirrors 2001-02-24
Diffraction Radiation
Monochromator Protocol
Two crystal monochromator (non-dispersive geometry) with Si(111) crystals MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X8C 0.9795 NSLS X8C

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 92.5 0.068 -- -- 5.2 14403 75176 -- -- 46.5
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)
2.6 2.69 94.2 -- -- -- -- --

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
MAD 2.6 38.34 -- 0.0 14403 13324 1347 92.5 0.241 0.241 0.241 0.287 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 2.76 -- 221 1839 0.335 0.405 0.027 87.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 54.5
Anisotropic B[1][1] -1.91
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.91
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.81
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.3
c_dihedral_angle_d 21.9
c_scbond_it 10.39
c_scangle_it 15.0
c_improper_angle_d 0.78
c_mcangle_it 14.77
c_bond_d 0.007
c_mcbond_it 9.53
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.39
Luzzati Sigma A (Observed) 0.38
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.5
Luzzati Sigma A (R-Free Set) 0.4
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2545
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 1

Software

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