X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 295.0
Details Sodium Acetate, Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.01 α = 90
b = 87.01 β = 90
c = 224.1 γ = 90
Symmetry
Space Group I 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRANDEIS - B4 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 -- NSLS X25

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
1.7 17 93.1 0.063 -- -- 5.8 -- 44403 0.0 -2.0 23.4
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)
1.7 -- 72.7 0.089 -- 7.2 -- --

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 1.7 9.95 -- 0.0 43541 43541 4366 91.6 -- -- 0.223 0.241 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 1.7 1.81 -- 580 5181 0.284 0.284 0.012 74.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 22.0
Anisotropic B[1][1] 2.71
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.71
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.42
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.95
c_scbond_it 1.95
c_mcangle_it 1.84
c_mcbond_it 1.17
c_improper_angle_d 0.76
c_dihedral_angle_d 22.4
c_angle_deg 1.3
c_bond_d 0.004
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) -0.02
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2026
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 235

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
AMoRE model building