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 = 84.67 α = 90
b = 84.67 β = 90
c = 160.04 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
AREA DETECTOR SIEMENS HI-STAR -- --
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
1.89 43.14 84.7 0.08 -- -- 7.4 45480 45480 0.0 0.0 11.1
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)
1.89 2.01 65.9 0.258 -- -- 2.43 5850

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
-- 1.89 43.14 0.0 0.0 45480 45480 4584 84.7 -- -- 0.219 0.257 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 1.89 2.01 -- 579 5271 0.296 0.331 0.014 65.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 25.7
Anisotropic B[1][1] 1.97
Anisotropic B[1][2] 4.35
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.97
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.94
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.87
c_scbond_it 2.0
c_mcangle_it 2.05
c_mcbond_it 1.35
c_improper_angle_d 0.76
c_dihedral_angle_d 22.6
x_angle_deg 1.4
x_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.24
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.3
Luzzati Sigma A (R-Free Set) 0.28
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4043
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 289

Software

Computing
Computing Package Purpose
FRAMBO, SIEMENS Data Reduction (intensity integration)
SAINT Data Reduction (data scaling)
CNS Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
CNS model building