X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Details MPD, Spermine, Glycerol, tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 28.75 α = 90
b = 42.4 β = 92.87
c = 33.14 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC Yale mirrors 1999-02-10
Diffraction Radiation
Monochromator Protocol
Yale Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
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
2 30 96.0 0.048 4.7 -- 4.9 4369 4125 0.0 0.0 41.4
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)
2.18 2.26 94.0 0.384 27.7 2.6 4.1 440

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
MIR 2.18 8.0 0.0 0.0 4145 3980 410 96.0 -- -- 0.253 0.276 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 2.18 2.31 -- 69 -- 0.427 0.457 0.055 93.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anistropic
Mean Isotropic B 58.0
Anisotropic B[1][1] 22.18
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 12.48
Anisotropic B[2][2] -15.43
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.75
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.49
c_dihedral_angle_d 12.7
c_angle_deg 1.2
c_bond_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.36
Luzzati Sigma A (Observed) 0.54
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.47
Luzzati Sigma A (R-Free Set) 0.56
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 546
Heterogen Atoms 0
Solvent Atoms 22

Software

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