X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 300.5
Details 12% PEG4000, 110MM Tris.HCl pH 7.4, 10% glycerol, 50mm magnesium acetate, 100MM ammonium acetate, 5MM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 300.5K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.76 α = 90
b = 223.88 β = 90
c = 43.02 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2001-06-30
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM14 0.9185 ESRF BM14

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 38 91.4 0.081 -- -- 6.4 29278 26760 0.0 0.0 114.6
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)
2.9 3.0 52.9 0.31 -- 3.1 4.1 --

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
MAD 2.9 37.84 -- 0.0 29278 24466 1228 83.6 0.264 0.264 0.264 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 2.9 3.12 -- 153 2941 0.375 0.419 0.034 53.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 98.2
Anisotropic B[1][1] 50.12
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -23.86
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -26.26
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.52
c_scbond_it 1.56
c_mcangle_it 2.42
c_mcbond_it 1.45
c_improper_angle_d 1.24
c_dihedral_angle_d 17.5
c_angle_deg 1.1
c_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.46
Luzzati Sigma A (Observed) 0.61
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.56
Luzzati Sigma A (R-Free Set) 0.6
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 727
Nucleic Acid Atoms 2706
Heterogen Atoms 26
Solvent Atoms 30

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE, SHARP, SOLOMON, EDEN, CNS Structure Solution
CNS 1.1, REFMAC Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
CNS model building
REFMAC model building
EDEN model building
SOLOMON model building
SHARP model building
SOLVE model building