X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 295.0
Details PEG 6000, tris, sodium acetate, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 37.47 α = 90
b = 97.6 β = 103.63
c = 53.09 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH Bent mirror 2002-10-04
Diffraction Radiation
Monochromator Protocol
Triangular monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8110 EMBL/DESY, Hamburg X11

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
1.87 25 95.8 0.056 -- -- 3.7 29394 29394 -- 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)
1.87 2.0 88.7 0.294 -- 4.5 3.2 4909

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 1.87 24.25 -- 0.0 29394 27922 1470 100.0 0.19369 0.19369 0.19119 0.2402 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 1.87 1.918 -- 86 1631 0.449 0.473 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.144
Anisotropic B[1][1] -0.2
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.47
Anisotropic B[2][2] -0.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.47
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.326
r_mcbond_it 0.709
r_nbtor_other 0.085
r_mcangle_it 1.341
r_nbd_refined 0.214
r_bond_refined_d 0.011
r_chiral_restr 0.084
r_xyhbond_nbd_refined 0.199
r_metal_ion_refined 0.023
r_symmetry_vdw_refined 0.253
r_angle_refined_deg 1.318
r_gen_planes_refined 0.004
r_gen_planes_other 0.002
r_symmetry_vdw_other 0.288
r_scbond_it 2.062
r_symmetry_hbond_refined 0.264
r_nbd_other 0.247
r_angle_other_deg 0.829
r_scangle_it 3.523
r_bond_other_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3044
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 273

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.29
MAR345 data collection
XDS data scaling
CNS phasing