X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.1
Temperature 291.0
Details PEG 4000, 2-propanol, MES, EDTA, beta-mercaptoethanol, NaN3, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.39 α = 90
b = 66.39 β = 90
c = 47.33 γ = 90
Symmetry
Space Group P 43

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRANDEIS - B4 monochromator 1999-11-13
Diffraction Radiation
Monochromator Protocol
parallel silicon crystal pair MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12C 1.14, 1.1724, 1.1719, 1.19 NSLS X12C

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
2.5 30 97.0 -- 0.042 -- 4.5 7168 7101 4.0 7.3 54.4
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)
2.5 2.6 98.1 -- 0.175 3.2 2.4 1373

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 2.5 30.0 0.0 2.0 7263 7101 777 97.0 0.222 0.22 0.216 0.275 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 2.5 2.59 719 68 -- 0.253 0.291 0.038 98.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 50.9
Anisotropic B[1][1] -0.9
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.9
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.81
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.83
c_dihedral_angle_d 23.8
c_bond_d 0.008
c_angle_deg 1.98
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Sigma A (Observed) 0.22
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.44
Luzzati Sigma A (R-Free Set) 0.37
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1515
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 21

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK, CCP4 (TRUNCATE) Data Reduction (data scaling)
SOLVE/RESOLVE Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
CNS refinement
RESOLVE model building
SOLVE model building