X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details PEG 8000, AMMONIUM CHLORIDE, TRIS, PH 8.5, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.62 α = 90
b = 60.62 β = 90
c = 63.73 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm BENT, VERTICALLY FOCUSING MIRROR 2005-01-26
Diffraction Radiation
Monochromator Protocol
Si [111], horizontally focusing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8034 EMBL/DESY, Hamburg X13

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
1.65 20 98.4 -- 0.056 -- 2.9 15827 15827 -- -3.0 --
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)
1.65 1.73 99.2 -- 0.262 4.3 2.5 2107

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
rigid body refinement 1.65 20.0 -- 0.0 15826 14973 853 98.44 -- 0.1683 0.1668 0.1945 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 1.65 1.693 -- 72 1111 0.237 0.301 -- 99.16
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS and isotropic individual
Mean Isotropic B 26.6316
Anisotropic B[1][1] 0.67
Anisotropic B[1][2] 0.34
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.67
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.01
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.219
r_symmetry_vdw_refined 0.24
r_chiral_restr 0.128
r_xyhbond_nbd_refined 0.171
r_mcangle_it 5.223
r_dihedral_angle_3_deg 11.317
r_gen_planes_refined 0.008
r_dihedral_angle_4_deg 27.458
r_bond_refined_d 0.018
r_nbd_refined 0.239
r_scangle_it 8.845
r_scbond_it 6.526
r_angle_refined_deg 2.196
r_dihedral_angle_2_deg 34.366
r_nbtor_refined 0.327
r_metal_ion_refined 0.026
r_dihedral_angle_1_deg 6.206
r_mcbond_it 4.827
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 828
Nucleic Acid Atoms 0
Heterogen Atoms 37
Solvent Atoms 111

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 3.10
MAR345 data collection
XDS data reduction
XSCALE data scaling
REFMAC phasing version: 5.2.0005