X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 2
Details pH 2.0 THE CRYSTALS WERE SOAKED AT PH=2.0 AND WERE STABLIZED BY GLUTARALDEHYDE CROSSLINKING.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.65 α = 90
b = 44.65 β = 90
c = 98.1 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE -- MIRRORS --
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
2.2 10 86.0 0.07 -- -- 2.5 -- 4968 -- -- 33.8
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)
2.2 2.4 86.0 -- -- -- -- --

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 2.3 10.0 -- 1.0 -- 4968 472 82.0 -- -- 0.245 0.27 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 2.3 2.42 -- 56 433 0.282 0.329 0.044 65.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 25.4
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 9.38
x_scbond_it 6.25
x_mcangle_it 5.34
x_mcbond_it 3.55
x_improper_angle_d 2.14
x_bond_d 0.01
x_angle_deg 1.17
x_dihedral_angle_d 24.7
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.37
Luzzati Sigma A (Observed) 0.44
Luzzati Resolution Cutoff (Low) 3.8
Luzzati ESD (R-Free Set) 0.4
Luzzati Sigma A (R-Free Set) 0.38
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 905
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 18

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
MARSCALE Data Reduction (data scaling)
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
MARSCALE data reduction
XDS data collection