X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details 4 MICROLITERS PROTEIN (14 MG/ML IN 50 MM TRIS/CL, 1 MM EDTA, 5 MM DTT, 10% (V/ V) GLYCEROL, PH 7.5) WERE MIXED WITH 4 MICROLITERS RESERVOIR SOLUTION (1.7-1.9 M LITHIUM SULFATE, 0.1 M MES, 0.5% (W/V) BETA-OCTYLGLUCOSIDE, PH 6.0) AND EQUILIBRATED AGAINST 1 ML OF RESERVOIR SOLUTION AT 293 K., VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 134.74 α = 90
b = 134.74 β = 90
c = 106.7 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 138
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC -- 1999-06-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID -- APS 19-ID

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
1.5 41.82 99.6 0.07 7.0 -- 7.5 -- 176690 -- -3.0 23.3
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)
1.5 1.53 93.3 0.729 72.9 1.3 3.1 --

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
SIRAS 1.5 41.9 -- 0.0 -- 156707 2393 88.1 -- 0.252 0.252 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 1.5 1.59 -- 346 21504 0.365 0.358 0.019 74.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 33.1
Anisotropic B[1][1] 3.38
Anisotropic B[1][2] 1.98
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.38
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.76
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.05
c_bond_d 0.012
c_angle_deg 1.5
c_dihedral_angle_d 23.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.16
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4057
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 336

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS 0.5 Structure Solution
CNS 0.5 Structure Refinement
Software
Software Name Purpose
CNS version: 0.5 refinement
CNS-V0.5 model building