X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details MPD, 40mM Na cacodylate (pH 6.0), 12 mM spermine 4HCl, 80 mM KCl, 20 mM BaCl2, VAPOR DIFFUSION, HANGING DROP at 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.99 α = 90
b = 39.99 β = 90
c = 52.62 γ = 90
Symmetry
Space Group P 43

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 98
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC Osmic confocal optics 2000-06-05
Diffraction Radiation
Monochromator Protocol
Osmic Confocal Optics SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 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
1.85 20 99.7 0.092 -- -- 4.6 7152 7128 -- -3.0 25.8
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)
1.85 1.88 98.4 0.4 -- 1.8 4.6 369

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 1.85 20.0 -- 2.0 -- 6991 756 97.9 -- 0.203 0.203 0.222 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 1.85 1.97 -- 123 1000 0.244 0.277 0.025 95.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 29.0
Anisotropic B[1][1] -0.03
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.05
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 10.3
c_improper_angle_d 1.34
c_bond_d 0.004
c_angle_deg 0.9
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.17
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.23
Luzzati Sigma A (R-Free Set) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 460
Heterogen Atoms 2
Solvent Atoms 69

Software

Software
Software Name Purpose
DENZO data reduction
Scalepack/Truncate data reduction
CNS refinement
SCALEPACK data scaling
CCP4 data scaling version: (TRUNCATE)
CNS phasing