X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.8
Temperature 278.0
Details 100 mM Na-acetate, 6% PEG 4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP at 278K, temperature 278.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 84.16 α = 90
b = 84.16 β = 90
c = 159.74 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
1.9 25.45 88.4 0.12 -- -- 12.0 46313 46313 0.0 0.0 29.6
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)
1.9 2.02 54.5 0.62 -- -- 5.5 4675

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
-- 1.9 25.45 0.0 0.0 46313 46313 4672 88.4 -- -- 0.197 0.222 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 1.9 2.02 -- 481 4208 0.338 0.348 0.016 54.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 34.3
Anisotropic B[1][1] 3.24
Anisotropic B[1][2] 3.42
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.24
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.47
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.95
c_scbond_it 2.03
c_mcangle_it 1.84
c_mcbond_it 1.23
c_improper_angle_d 0.84
c_dihedral_angle_d 22.5
x_angle_deg 1.3
x_bond_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) 0.19
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.21
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4074
Nucleic Acid Atoms 0
Heterogen Atoms 39
Solvent Atoms 223

Software

Computing
Computing Package Purpose
R-AXIS Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement