X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 277.0
Details 22% PEG 4000, 100 mM MES pH 5.6, 200 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.84 α = 67.91
b = 63.51 β = 79.76
c = 64.05 γ = 84.88
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Sagitally focusing Ge(220) and a multilayer 2002-07-10
Diffraction Radiation
Monochromator Protocol
Diamond (111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1

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
1.7 30 92.9 -- 0.09 -- 4.4 61592 61592 0.0 -3.0 21.6
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)
1.7 1.8 75.8 -- 0.509 2.84 3.6 7906

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 1.75 29.41 -- 0.0 57712 57712 2886 95.2 -- 0.21 0.21 0.242 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 1.75 1.86 8353 439 8353 0.275 0.307 0.015 87.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 30.0
Anisotropic B[1][1] 0.83
Anisotropic B[1][2] 1.1
Anisotropic B[1][3] 2.57
Anisotropic B[2][2] 1.36
Anisotropic B[2][3] -3.22
Anisotropic B[3][3] -2.19
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.87
c_bond_d 0.008
c_mcangle_it 2.23
c_scbond_it 1.97
c_scangle_it 2.95
c_angle_deg 1.4
c_dihedral_angle_d 21.8
c_mcbond_it 1.39
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.16
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4664
Nucleic Acid Atoms 0
Heterogen Atoms 106
Solvent Atoms 231

Software

Software
Software Name Purpose
CNS refinement version: 1.1
XDS data reduction
XSCALE data scaling
AMoRE phasing