X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.4
Temperature 293.0
Details 50 mM tris HCl (pH 6.4), 1.4 M (NH4)2SO4, 20 mM MgCl2, 18 mM spermine, neomycin B, pH 6.4, VAPOR DIFFUSION, HANGING DROP at 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.23 α = 90
b = 44.23 β = 90
c = 49.87 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 2000-05-31
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
1.8 99 99.8 0.102 -- -- 9.9 9161 9145 -- -3.0 30.2
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)
1.8 1.83 100.0 0.51 -- 3.7 9.3 447

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 1.8 21.72 -- 2.0 -- 8800 911 97.9 -- 0.215 0.215 0.241 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 1.8 1.91 -- 136 1288 0.266 0.3 0.026 96.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 24.8
Anisotropic B[1][1] 0.88
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.88
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.76
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.004
c_angle_deg 0.8
c_dihedral_angle_d 11.1
c_improper_angle_d 1.18
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.17
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.27
Luzzati Sigma A (R-Free Set) 0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 460
Heterogen Atoms 2
Solvent Atoms 74

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement
CNS phasing