X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 298.0
Details PEG 6000, potassium phosphate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 29.7 α = 90
b = 59.9 β = 90
c = 65.4 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC -- 1999-10-15
IMAGE PLATE RIGAKU RAXIS IIC -- 1999-10-12
IMAGE PLATE RIGAKU RAXIS IIC -- 1999-10-10
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200BH 1.5418 -- --
ROTATING ANODE RIGAKU RU200BH 1.5418 -- --
ROTATING ANODE RIGAKU RU200HB 1.5418 -- --

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
1.7 20 98.6 0.07 -- -- 16.9 13248 13248 2.0 0.0 21.9
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)
1.7 20.0 88.4 0.32 -- 149.0 10.0 1169

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
SAD, MIR,MOLECULAR REPLACEMENT 1.7 20.0 0.0 2.0 13248 12801 1079 95.4 -- -- 0.19 0.21 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 1.7 1.76 907 81 -- 0.2661 0.2626 -- 88.4
X Ray Diffraction 1.76 1.83 1039 122 -- 0.2391 0.2539 -- 97.9
X Ray Diffraction 1.83 1.91 1117 139 -- 0.1955 0.1812 -- 100.0
X Ray Diffraction 1.91 2.02 1154 135 -- 0.2002 0.2201 -- 100.0
X Ray Diffraction 2.02 2.14 1174 124 -- 0.1957 0.1886 -- 100.0
X Ray Diffraction 2.14 2.31 1196 132 -- 0.2093 0.2104 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.2
Anisotropic B[1][1] -0.5
Anisotropic B[1][2] -0.05
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.47
c_dihedral_angle_d 21.4
c_bond_d 0.006
c_angle_deg 1.3
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.08
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.19
Luzzati Sigma A (R-Free Set) 0.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 892
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 87

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
CNS refinement
CNS model building