X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details Ammonium Sulfate, Magnesium Sulfate, Cacodylate Na, 1,8-diaminooctane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 411.81 α = 90
b = 411.81 β = 90
c = 81.97 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 1998-04-24
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.708 SPring-8 BL41XU

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
2.9 50 96.5 -- -- -- -- 150310 150310 0.0 0.0 56.5
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)
2.9 3.08 87.9 -- -- -- -- --

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
MIR 2.9 40.0 -- 0.0 150310 150310 7532 96.5 -- 0.248 0.248 0.282 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 2.9 3.08 -- 1136 21386 0.376 0.381 0.011 87.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 50.8
Anisotropic B[1][1] 8.51
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 8.51
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -17.02
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 3.62
c_mcbond_it 2.56
c_improper_angle_d 1.16
c_mcangle_it 4.2
c_dihedral_angle_d 22.1
c_bond_d 0.008
c_angle_deg 1.4
c_scangle_it 5.66
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.43
Luzzati Sigma A (Observed) 0.77
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.49
Luzzati Sigma A (R-Free Set) 0.8
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13940
Nucleic Acid Atoms 3206
Heterogen Atoms 60
Solvent Atoms 218

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MLPHARE phasing
CNS refinement version: 1.0