X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.7
Temperature 289.0
Details sodium acetate, PEG 4000, ZnSO4, pH 4.7, temperature 289K, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.85 α = 90
b = 85.04 β = 90
c = 134.92 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 MARMOSAIC 225 mm CCD -- 2006-02-23
Diffraction Radiation
Monochromator Protocol
Si(111) channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM14 1.033 ESRF BM14

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
2.18 43 95.0 0.109 -- -- 3.8 -- 34837 -- -- --
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)
2.18 2.26 95.2 0.421 -- -- 3.2 3419

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 2.18 27.77 -- 0.0 -- 32926 1753 89.8 -- -- 0.2 0.24 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 2.18 2.32 -- 371 4722 0.251 0.271 0.014 84.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 21.6
Anisotropic B[1][1] 2.79
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.9
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.11
RMS Deviations
Key Refinement Restraint Deviation
c_mcbond_it 1.26
c_angle_deg 1.4
c_bond_d 0.011
c_scbond_it 2.05
c_mcangle_it 2.0
c_dihedral_angle_d 22.2
c_improper_angle_d 1.17
c_scangle_it 2.95
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.22
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.29
Luzzati Sigma A (R-Free Set) 0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4749
Nucleic Acid Atoms 0
Heterogen Atoms 127
Solvent Atoms 233

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
EPMR phasing version: 2.5
CNS refinement version: 1.2
PDB_EXTRACT data extraction version: 3.004
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling