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 = 98.71 α = 90
b = 98.71 β = 90
c = 80.6 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 84.51 99.79 0.129 -- -- 5.0 28657 28657 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)
2.0 2.052 99.8 0.702 -- 2.3 4.9 4221

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 2.0 84.51 0.0 0.0 28657 28657 1524 99.79 0.19445 0.19445 0.19322 0.21776 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 2.0 2.052 4221 110 2145 0.301 0.309 -- 99.8
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.881
Anisotropic B[1][1] 1.55
Anisotropic B[1][2] 0.77
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.55
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.32
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.004
r_dihedral_angle_1_deg 3.049
r_mcbond_it 0.58
r_symmetry_hbond_refined 0.188
r_angle_refined_deg 1.361
r_symmetry_vdw_refined 0.283
r_scangle_it 2.452
r_scbond_it 1.418
r_angle_other_deg 0.823
r_gen_planes_other 0.003
r_nbd_other 0.24
r_bond_other_d 0.002
r_xyhbond_nbd_refined 0.143
r_nbd_refined 0.205
r_mcangle_it 1.098
r_bond_refined_d 0.01
r_symmetry_vdw_other 0.263
r_nbtor_other 0.08
r_chiral_restr 0.087
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.142
Luzzati ESD (R-Free Set) 0.13
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2230
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 192

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