X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.2
Temperature 295.0
Details PEG 4000, SODIUM-ACETATE TRIHYDRATE, 2,2'-Anhydrouridine, sodium phosphate , pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.88 α = 90
b = 124.07 β = 90
c = 134.4 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 mirrors 2004-06-19
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6

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
2.11 28.75 97.4 0.121 -- -- 3.09 -- 86174 0.0 0.0 10.4
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)
2.11 2.15 90.4 0.325 -- 3.87 2.85 6430

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 2.11 28.75 -- 2.0 -- 83853 4192 97.5 0.182 0.18 0.18 0.219 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 2.11 2.24 13514 671 12843 0.217 0.273 0.011 95.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 21.2
Anisotropic B[1][1] 2.74
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.6
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.34
RMS Deviations
Key Refinement Restraint Deviation
c_mcbond_it 2.6
c_scangle_it 7.27
c_scbond_it 4.75
c_angle_deg 1.5
c_bond_d 0.007
c_improper_angle_d 0.83
c_mcangle_it 3.94
c_dihedral_angle_d 23.9
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.18
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.23
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10937
Nucleic Acid Atoms 0
Heterogen Atoms 47
Solvent Atoms 641

Software

Software
Software Name Purpose
CNS refinement version: 1.1
MAR345 data collection
XDS data scaling
MOLREP phasing version: V. 7.3