X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details PEG 4000, NaCl, ADA, MgCl2, HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.41 α = 90
b = 146.22 β = 90
c = 46.78 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 108
2 108
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Yale mirrors 2001-04-05
CCD ADSC QUANTUM 315 -- 2002-02-02
Diffraction Radiation
Monochromator Protocol
Ni Filter SINGLE WAVELENGTH
Si 111 Channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --
SYNCHROTRON NSLS BEAMLINE X25 1.1123 NSLS X25

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 50 93.2 -- -- -- -- 24798 23122 -- -3.0 --
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)
2.0 2.1 76.1 -- 0.15 5.8 3.1 2691

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 2.0 50.0 -- 0.0 24798 23122 1249 93.2 0.241 0.241 0.24 0.269 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 2.0 2.1 -- 1249 -- 0.215 0.245 -- 76.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 42.8
RMS Deviations
Key Refinement Restraint Deviation
p_planar_tor 23.0
p_angle_d 1.3
p_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.29
Luzzati Sigma A (Observed) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2039
Nucleic Acid Atoms 650
Heterogen Atoms 0
Solvent Atoms 145

Software

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