X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.2
Temperature 293.0
Details sodium acetate, ammonium acetate, PEG 4000, glycerol, uridine-5'-monophosphate, dithiothreitol, pH 8.2, VAPOR DIFFUSION, HANGING DROP at 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 91.83 α = 90
b = 113.76 β = 90
c = 126.59 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Osmic mirrors 2001-12-01
Diffraction Radiation
Monochromator Protocol
Ni filter SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 1.5418 -- --

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
2.05 100 97.4 0.115 -- -- 8.1 40722 40722 -1.73 -3.0 14.3
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)
2.05 2.12 95.5 0.509 -- 4.1 -- 3949

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 2.05 19.78 0.0 0.0 39951 39951 2005 95.5 0.182 0.182 0.182 0.226 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 2.05 2.18 -- 341 5902 0.209 0.264 0.014 90.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 28.1
Anisotropic B[1][1] 1.94
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.68
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.62
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.71
c_scbond_it 2.66
c_mcangle_it 2.13
c_mcbond_it 1.53
c_improper_angle_d 1.0
c_dihedral_angle_d 25.5
c_angle_deg 1.6
c_bond_d 0.013
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.14
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.18
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4007
Nucleic Acid Atoms 0
Heterogen Atoms 187
Solvent Atoms 325

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
EPMR Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
EPMR model building
SCALEPACK data reduction
DENZO data collection