X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 285.0
Details (NH4)2SO4, NaOAc, DTT, 2',3'-cyclic uridine vanadate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 101.14 α = 90
b = 101.14 β = 90
c = 90 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-03-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B 1.070 NSLS X9B

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
2.4 50 90.3 0.048 -- -- 3.0 7212 7212 -- 0.0 38.4
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)
2.4 2.49 95.4 0.466 -- -- 3.0 --

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 2.4 25.29 -- 0.0 -- 5960 650 84.2 -- -- 0.214 0.399 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 2.4 2.55 -- 97 829 0.431 0.477 0.048 79.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 59.9
Anisotropic B[1][1] 0.85
Anisotropic B[1][2] 6.95
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.85
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.71
RMS Deviations
Key Refinement Restraint Deviation
c_mcbond_it 2.65
c_mcangle_it 4.24
c_scbond_it 4.09
c_improper_angle_d 1.02
c_bond_d 0.013
c_dihedral_angle_d 25.2
c_scangle_it 6.01
c_angle_deg 2.1
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.42
Luzzati Sigma A (Observed) 0.64
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.59
Luzzati Sigma A (R-Free Set) 0.85
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1458
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 94

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
CNS refinement version: 1.0