X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.6
Details 0.2 M AMMONIUM ACETATE, 30% W/V PEG 4000, 0.1 M SODIUM CITRATE PH 5.6, PROTEIN CONCENTRATION 15 MG/ML PLUS 10 MM DTT, TEMPERATURE 297 K, FOR CRYOPROTECTION 10% OF PEG 400 WAS ADDED.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.47 α = 115.25
b = 42.84 β = 97.3
c = 49.77 γ = 102.4
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU IMAGE PLATE RAXIS V MIRRORS 2001-06-17
Diffraction Radiation
Monochromator Protocol
DIAMOND SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL45XU -- SPring-8 BL45XU

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
1.52 30 93.9 0.103 -- -- 3.103 -- 40937 -- 0.0 16.0
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)
1.52 1.55 87.1 0.484 -- 2.021 -- --

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 1.53 28.5 -- 0.0 -- 40277 2010 93.2 -- 0.208 0.208 0.235 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 1.53 1.63 -- 318 5884 0.328 0.319 0.018 85.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 21.8
Anisotropic B[1][1] 1.17
Anisotropic B[1][2] -2.39
Anisotropic B[1][3] 1.35
Anisotropic B[2][2] -0.94
Anisotropic B[2][3] -0.7
Anisotropic B[3][3] -0.24
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 21.0
c_scbond_it 2.75
c_angle_deg 1.1
c_improper_angle_d 0.72
c_bond_d 0.005
c_mcangle_it 2.75
c_scangle_it 4.01
c_mcbond_it 1.79
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.26
Luzzati Resolution Cutoff (Low) 20.0
Luzzati ESD (R-Free Set) 0.22
Luzzati Sigma A (R-Free Set) 0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2361
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 293

Software

Software
Software Name Purpose
CNS refinement version: 1.0
DENZO data reduction
SCALEPACK data scaling
X-PLOR phasing