X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.2
Details VAPOUR DIFFUSION (HANGING DROPS), WELLS: 500 MICROLITRES (14% PEG4000, 6% MPD), DROPS: 5 MICROLITRES PROTEIN (5 MG/ML IN 50 MM K2HPO4/ KH2PO4, PH= 6.2),5 MICROLITRES WELL SOL. PLUS 1 MICROLITRE OF P-CL-MERCURIBENZOATE (=1 MM IN WATER), THIN LARGE CRYSTAL PRISMS APPEAR AT 295 DEGREES KELVIN IN 1 MONTH., pH 6.20

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.87 α = 90
b = 55.53 β = 90
c = 96.07 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 -- 2000-07-15
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 1.0090, 1.0120 EMBL/DESY, Hamburg X31

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
2.75 48.2 97.7 0.081 -- -- 5.2 -- 8343 -- 2.1 45.9
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)
2.75 2.9 97.8 0.32 -- 2.1 5.3 --

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
MAD 2.75 27.89 -- 0.0 -- 7421 806 96.6 -- 0.238 0.238 0.272 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 2.75 2.92 -- 125 1110 0.342 0.378 0.034 97.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 48.1
Anisotropic B[1][1] 5.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.99
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -12.08
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.4
c_improper_angle_d 0.89
c_bond_d 0.008
c_dihedral_angle_d 22.6
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.38
Luzzati Sigma A (Observed) 0.4
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.47
Luzzati Sigma A (R-Free Set) 0.51
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2026
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 30

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
CNS phasing
SHARP phasing
CNS refinement version: 1.1