X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 277.0
Details MPD, magnesium acetate, spermine, sodium cacodylate. pH 7.0, VAPOR DIFFUSION, HANGING DROP at 277 K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 25.18 α = 90
b = 40.88 β = 90
c = 63.73 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
DIFFRACTOMETER WEISSENBERG -- 1999-04-18
DIFFRACTOMETER WEISSENBERG -- 2000-12-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-18B 1.0 Photon Factory BL-18B
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6B 1.0 Photon Factory BL-6B

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
1.6 100 97.6 0.08 -- -- -- 9068 9068 -- -3.0 13.5
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)
1.6 1.66 93.9 -- -- -- -- 759

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 1.6 10.0 -- 0.0 8895 8895 936 97.6 -- -- 0.224 0.256 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 1.6 1.66 -- 74 759 0.376 0.429 0.05 93.8
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.5
Anisotropic B[1][1] 1.96
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.72
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.24
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 21.7
c_angle_deg 0.9
c_bond_d 0.004
c_improper_angle_d 1.41
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.25
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.31
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 486
Heterogen Atoms 11
Solvent Atoms 104

Software

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