X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 9
Details HANGING DROP CONSISTING OF 2 UL OF PROTEIN (31.2 MG/ML) AND 2 UL RESERVOIR (0.1 M TRIS-HCL PH9.0, 1.6 M AMMONIUM SULPHATE), pH 9.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.51 α = 90
b = 85.85 β = 90
c = 89.64 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A -- Photon Factory BL-6A

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
1.62 35.35 81.6 0.056 -- -- 5.3 -- 60922 -- -- 15.3
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)
1.62 1.68 83.9 0.289 -- -- 4.9 --

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
MIRAS 1.62 34.94 -- 0.0 -- 67019 6796 88.5 -- 0.159 0.159 0.177 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 1.62 1.72 -- 1062 9295 0.193 0.216 0.007 83.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 16.2
Anisotropic B[1][1] 3.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.91
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 1.78
c_improper_angle_d 0.8
c_angle_deg 1.2
c_mcangle_it 1.62
c_scangle_it 2.59
c_mcbond_it 1.06
c_dihedral_angle_d 23.5
c_bond_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.15
Luzzati Sigma A (Observed) 0.09
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.17
Luzzati Sigma A (R-Free Set) 0.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4746
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 389

Software

Software
Software Name Purpose
CNS refinement version: 1.1
DENZO data reduction
Agrovata data scaling
ROTAVATA data scaling
SHARP phasing
ARP phasing
DM phasing