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 = 60.88 α = 90
b = 60.88 β = 90
c = 63.87 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2005-02-01
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 BW7B 0.8430 EMBL/DESY, Hamburg BW7B

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 20 97.8 -- 0.06 -- 2.4 8979 8979 -- -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)
2.0 2.1 98.7 -- 0.493 2.6 2.4 1239

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 2.0 20.0 -- -- 8493 8493 482 97.86 -- 0.16473 0.16241 0.20407 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 -- 35 646 0.241 0.339 -- 98.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS and isotropic individual
Mean Isotropic B 34.695
Anisotropic B[1][1] 1.81
Anisotropic B[1][2] 0.91
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.81
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.72
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.196
r_chiral_restr 0.121
r_dihedral_angle_4_deg 31.503
r_dihedral_angle_3_deg 16.126
r_dihedral_angle_2_deg 45.512
r_bond_refined_d 0.019
r_dihedral_angle_1_deg 7.188
r_symmetry_vdw_refined 0.225
r_angle_refined_deg 1.885
r_mcangle_it 2.656
r_nbtor_refined 0.32
r_scangle_it 10.286
r_scbond_it 7.393
r_nbd_refined 0.228
r_mcbond_it 1.527
r_symmetry_hbond_refined 0.159
r_gen_planes_refined 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 814
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 96

Software

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