X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details sodium citrate, ammonium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.33 α = 90
b = 56.44 β = 90
c = 72.76 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2002-04-04
Diffraction Radiation
Monochromator Protocol
triangular monochromator, bent mirror single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.9073 EMBL/DESY, HAMBURG X11

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
1.8 14 98.3 -- 0.037 -- 3.6 22112 21938 0.0 -3.0 13.5
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)
1.8 1.86 87.8 -- 0.116 4.5 3.4 1941

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 1.8 14.0 -- 0.0 21938 21938 1103 -- 0.184 0.184 0.182 0.221 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 1.8 1.86 2138 100 -- 0.21 0.247 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 15.3
Anisotropic B[1][1] 3.6
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.1
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.5
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 1.322
c_scbond_it 0.867
c_mcangle_it 0.979
c_mcbond_it 0.584
c_improper_angle_d 0.676
c_dihedral_angle_d 25.56
c_angle_deg 1.26
c_bond_d 0.0046
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.11
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2023
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 353

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 0.9 Structure Refinement
Software
Software Name Purpose
CNS version: 0.9 refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection