X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 293.0
Details PEG 6000, citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 130.27 α = 90
b = 130.27 β = 90
c = 84.49 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2000-12-14
Diffraction Radiation
Monochromator Protocol
YALE MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU ULTRAX 18 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
1.86 33.22 99.2 0.073 -- -- 4.6 30733 30496 0.0 0.0 26.1
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)
1.86 1.93 98.6 0.286 -- 2.4 4.6 2978

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 1.86 32.57 -- 0.0 30733 30496 1534 99.1 0.217 0.215 0.215 0.248 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 1.86 1.98 -- 274 4698 0.275 0.3 0.018 98.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 29.7
Anisotropic B[1][1] 1.42
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.84
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 5.7
c_scbond_it 4.13
c_mcangle_it 3.24
c_mcbond_it 2.53
c_improper_angle_d 0.67
c_bond_d 0.006
c_angle_deg 1.3
c_dihedral_angle_d 22.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) 0.16
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.27
Luzzati Sigma A (R-Free Set) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2021
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 174

Software

Computing
Computing Package Purpose
CRYSTALCLEAR V. 1.3 (MSC/RIGAKU) Data Reduction (intensity integration)
CRYSTALCLEAR V. 1.3 (MSC/RIGAKU) Data Reduction (data scaling)
MOLREP Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
MOLREP model building
CrystalClear version: 1.3 data reduction
CrystalClear version: 1.3 data collection