X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details sodium citrate, lithium chloride, potassium phosphate, adenosine, manganese chloride, PEG monomethylether 5000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.9 α = 90
b = 75.7 β = 90
c = 221.7 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1999-03-25
Diffraction Radiation
Monochromator Protocol
bent single-crystal germanium triangular monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.9116 EMBL/DESY, Hamburg X11

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 50 99.5 0.054 -- -- 3.5 69235 69235 0.0 0.0 20.4
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)
2.1 2.2 97.2 0.298 -- -- 3.1 --

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 2.1 29.56 0.0 0.0 69235 69235 2116 99.5 0.238 0.238 0.238 0.279 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 2.1 2.23 11035 367 11035 0.269 0.324 0.017 99.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 45.3
Anisotropic B[1][1] 3.87
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.85
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.99
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.6
c_improper_angle_d 1.11
c_bond_d 0.013
c_scbond_it 2.23
c_mcangle_it 2.11
c_mcbond_it 1.49
c_scangle_it 2.82
c_dihedral_angle_d 23.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.29
Luzzati Sigma A (Observed) 0.2
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.36
Luzzati Sigma A (R-Free Set) 0.28
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8200
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 355

Software

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