X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9.5
Temperature 300.0
Details 100 mM Ches, 400 mM ammonium sulfate, 35% OEG 6K, 1 mM manganese, 10 mM dAMP, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.29 α = 90
b = 88.74 β = 90
c = 145.12 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 ADSC QUANTUM 4 -- 2000-07-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.98400 SSRL BL9-2

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
2.2 30 98.1 0.046 -- -- 8.8 431781 431781 0.0 0.0 29.7
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)
2.2 2.25 86.1 0.326 -- -- 4.0 --

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
MAD 2.2 30.0 0.0 0.0 47867 47867 2397 97.7 0.222 0.222 0.222 0.264 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 2.2 2.34 -- 368 6548 0.336 0.375 0.02 85.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 44.8
Anisotropic B[1][1] -5.65
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 9.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.49
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 2.21
c_dihedral_angle_d 24.0
c_bond_d 0.013
c_mcbond_it 1.52
c_improper_angle_d 0.99
c_angle_deg 1.8
c_scangle_it 3.24
c_mcangle_it 2.48
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.32
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.37
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5501
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 264

Software

Software
Software Name Purpose
MLPHARE phasing
CNS refinement version: 1.0
DENZO data reduction
CCP4 data scaling version: (TRUNCATE)