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 0.1M Tris-HCl, 0.8M Potassium sodium tartrate, 2.5% PEG 5000, MME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 0.1M Tris-HCl, 0.8M Potassium sodium tartrate, 0.75% PEG 5000, MME, 5mM K2PtCl4, 16h soaking, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.24 α = 90
b = 60.24 β = 90
c = 171.28 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU JUPITER 210 Two dimensional focusing mirror 2005-04-16
CCD RIGAKU JUPITER 210 Two dimensional focusing mirror 2005-05-25
Diffraction Radiation
Monochromator Protocol
Si double crystal MAD
Si double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.00000 SPring-8 BL26B1
SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.07181, 1.07216, 1.05000 SPring-8 BL26B1

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
1.55 50 97.2 -- 0.071 -- 6.6 -- 45583 -- -3.0 19.9
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)
1.55 1.61 93.3 -- 0.282 5.05 4.1 4258

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 1.55 42.82 -- 0.0 -- 44576 4520 95.1 -- -- 0.182 0.209 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 1.55 1.65 6745 649 6096 0.213 0.251 0.01 88.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 20.7
Anisotropic B[1][1] -0.16
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.32
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 4.75
c_scbond_it 3.54
c_bond_d 0.01
c_mcangle_it 2.96
c_angle_deg 1.6
c_improper_angle_d 1.15
c_dihedral_angle_d 22.5
c_mcbond_it 2.34
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.16
Luzzati Sigma A (Observed) 0.09
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.19
Luzzati Sigma A (R-Free Set) 0.12
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2113
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 316

Software

Software
Software Name Purpose
CNS refinement version: 1.1
HKL-2000 data reduction
SCALEPACK data scaling
SOLVE phasing