X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details PEG 1000, HEPES, pH 7.5 , VAPOR DIFFUSION, HANGING DROP at 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 144.52 α = 90
b = 144.52 β = 90
c = 108.16 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2000-01-26
IMAGE PLATE MARRESEARCH -- 1999-09-26
Diffraction Radiation
Monochromator Protocol
Double crystal focussing monochromator MAD
channel-cut monochromator Si (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 1.7400 EMBL/DESY, HAMBURG BW7A
SYNCHROTRON ESRF BEAMLINE BM1A 0.9700 ESRF BM1A

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
2.6 50 82.4 -- 0.076 -- 3.3 87368 63971 -- 2.0 29.2
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)
2.6 2.69 65.1 -- 0.31 4.0 2.3 --

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 2.6 43.34 0.0 0.0 87368 63971 3219 82.3 -- 0.257 0.257 0.296 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 2.5 2.66 2991 121 2991 0.3 0.358 0.033 21.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 37.4
Anisotropic B[1][1] 4.78
Anisotropic B[1][2] 8.67
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.78
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -9.55
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 7.29
c_scbond_it 5.7
c_mcangle_it 5.44
c_mcbond_it 3.67
c_improper_angle_d 0.96
c_dihedral_angle_d 23.0
c_angle_deg 1.4
c_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.37
Luzzati Sigma A (Observed) 0.29
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.46
Luzzati Sigma A (R-Free Set) 0.4
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 16020
Nucleic Acid Atoms 0
Heterogen Atoms 348
Solvent Atoms 154

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
AMORE model building
SCALEPACK data reduction
DENZO data collection