X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 295.0
Details 18% (w/v) PEG 4000, 0.3 M NaCl, 0.1 M sodium acetate buffer (pH = 5.0), 5 mM 2-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 7.50

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.01 α = 90
b = 104.68 β = 90
c = 126.84 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 105
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV mirrors 2001-09-17
Diffraction Radiation
Monochromator Protocol
mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 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 40 99.7 -- 0.078 -- 4.3 77964 77907 -- 0.0 14.8
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)
2.0 2.07 97.7 -- 0.23 6.1 4.0 7499

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
MOLECULAR REPLACEMENT 2.0 35.67 -- 0.0 77964 77907 3949 99.9 0.221 0.2191 0.219 0.256 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 2.0 2.13 -- 650 12151 0.264 0.309 0.012 99.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 27.6
Anisotropic B[1][1] -8.99
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 14.8
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.82
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.42
c_scbond_it 2.38
c_mcangle_it 2.2
c_mcbond_it 1.51
c_improper_angle_d 0.93
c_bond_d 0.012
c_angle_deg 1.5
c_dihedral_angle_d 21.7
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.3
Luzzati Sigma A (R-Free Set) 0.24
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8674
Nucleic Acid Atoms 0
Heterogen Atoms 66
Solvent Atoms 577

Software

Computing
Computing Package Purpose
R-AXIS Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
CNS model building
SCALEPACK data reduction
R-AXIS data collection