X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 277.0
Details NA ACETATE, IMIDAZOLE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98.65 α = 90
b = 98.65 β = 90
c = 80.47 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.10000 ALS 8.3.1

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
2.85 84.51 99.79 0.138 -- -- 4.9 9976 9976 0.0 0.0 --
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)
2.85 2.92 100.0 0.776 -- 1.6 4.9 3799

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 2.85 84.51 0.0 0.0 9976 9976 501 99.79 0.21034 0.21034 0.20768 0.26166 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 2.85 2.92 3799 36 737 0.328 0.336 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.701
Anisotropic B[1][1] 5.8
Anisotropic B[1][2] 2.9
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.8
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.7
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.22
r_gen_planes_other 0.003
r_bond_refined_d 0.013
r_nbd_refined 0.211
r_bond_other_d 0.002
r_angle_refined_deg 1.545
r_symmetry_vdw_refined 0.112
r_symmetry_vdw_other 0.219
r_dihedral_angle_1_deg 2.949
r_nbtor_other 0.087
r_mcbond_it 0.427
r_angle_other_deg 0.868
r_xyhbond_nbd_refined 0.245
r_mcangle_it 0.82
r_scbond_it 1.091
r_scangle_it 1.953
r_chiral_restr 0.094
r_gen_planes_refined 0.005
r_symmetry_hbond_refined 0.131
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.363
Luzzati ESD (R-Free Set) 0.326
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2230
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 25

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.25
Blu-Ice data collection
MOSFLM data reduction
CCP4 data scaling version: (SCALA)
CCP4 phasing