X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 277.0
Details PEG 20000, magnesium chloride, ethylene glycol, Tris HCl, AMPPNP, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.4 α = 81.64
b = 58.64 β = 82.39
c = 148.87 γ = 87.43
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1999-10-20
Diffraction Radiation
Monochromator Protocol
Double Crystal Monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X26C 1.087 NSLS X26C

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
3 40 80.6 -- 0.077 -- 3.5 34823 31019 0.0 -3.0 39.8
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)
3.0 3.11 53.7 -- 0.472 5.6 2.1 1898

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 3.0 39.81 -- 1.0 29029 25462 1260 73.1 0.29812 0.2812 0.277 0.316 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 3.0 3.04 -- 17 426 0.415 0.414 0.1 31.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 77.1
Anisotropic B[1][1] -3.59
Anisotropic B[1][2] 1.99
Anisotropic B[1][3] -14.48
Anisotropic B[2][2] 17.22
Anisotropic B[2][3] 4.03
Anisotropic B[3][3] -13.63
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 19.21
c_scbond_it 16.16
c_mcangle_it 15.1
c_mcbond_it 10.46
c_improper_angle_d 2.09
c_bond_d 0.015
c_angle_deg 2.5
c_dihedral_angle_d 24.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.53
Luzzati Sigma A (Observed) 0.61
Luzzati Resolution Cutoff (Low) 40.0
Luzzati ESD (R-Free Set) 0.65
Luzzati Sigma A (R-Free Set) 0.8
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8235
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 7

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 0.9 Structure Refinement
Software
Software Name Purpose
CNS version: 0.9 refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection