X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 276.0
Details PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 276K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 102.17 α = 90
b = 56.75 β = 127.04
c = 74.89 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 1.0 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
2.78 30.9 99.2 -- 0.102 -- 3.2 -- 8472 -- 0.0 --

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 2.8 20.0 -- 0.0 -- 8056 394 100.0 -- 0.2399 0.2384 0.27105 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 2.8 2.871 -- 37 574 0.335 0.361 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.696
Anisotropic B[1][1] -0.41
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -3.6
Anisotropic B[2][2] 0.95
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.88
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.261
r_nbd_refined 0.277
r_gen_planes_other 0.003
r_gen_planes_refined 0.005
r_chiral_restr 0.084
r_dihedral_angle_2_deg 16.994
r_dihedral_angle_1_deg 2.383
r_angle_other_deg 0.808
r_angle_refined_deg 1.605
r_bond_other_d 0.001
r_bond_refined_d 0.016
r_xyhbond_nbd_refined 0.158
r_xyhbond_nbd_other 0.165
r_symmetry_vdw_refined 0.258
r_symmetry_vdw_other 0.308
r_symmetry_hbond_refined 0.318
r_mcbond_it 0.756
r_mcangle_it 1.386
r_scbond_it 1.6
r_scangle_it 2.724
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2873
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 75

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement