X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Both Sitting Drop and Hanging Drop
pH 4.8
Temperature 295.0
Details 2 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, POTASSIUM PHOSPHATE BUFFER, pH 4.8, VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 348.55 α = 90
b = 348.55 β = 90
c = 348.55 γ = 90
Symmetry
Space Group P 42 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 295
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1996-03-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 -- SSRL BL7-1

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
2.7 40 68.7 0.107 -- -- 3.2 178705 178705 0.0 0.0 23.7
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)
2.7 2.8 82.7 0.453 -- -- 2.5 --

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 2.7 40.0 1.5 3.0 178705 134454 13357 68.7 0.206 0.152 0.151 0.159 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 2.7 2.8 -- 716 6860 0.221 0.241 0.009 39.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 33.3
RMS Deviations
Key Refinement Restraint Deviation
x_bond_d 0.01
x_angle_deg_na 2.38
x_scbond_it 13.71
x_dihedral_angle_d_prot 20.3
x_dihedral_angle_d 20.3
x_angle_deg 1.9
x_improper_angle_d_na 2.93
x_mcbond_it 3.61
x_bond_d_prot 0.01
x_improper_angle_d 1.32
x_bond_d_na 0.015
x_angle_deg_prot 1.9
x_scangle_it 23.41
x_improper_angle_d_prot 1.32
x_mcangle_it 5.86
x_dihedral_angle_d_na 39.3
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.29
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.23
Luzzati Sigma A (R-Free Set) 0.32
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4203
Nucleic Acid Atoms 182
Heterogen Atoms 0
Solvent Atoms 285

Software

Software
Software Name Purpose
X-PLOR model building
X-PLOR refinement version: 3.851
DENZO data reduction
SCALEPACK data scaling
X-PLOR phasing