X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 279.0
Details 35 % (w/v) PEG4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 279K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.66 α = 115.28
b = 44.49 β = 98.61
c = 46.39 γ = 109.55
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2012-01-18
Diffraction Radiation
Monochromator Protocol
Si 111 double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.978 BESSY 14.2

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
1.2 50 91.7 0.035 -- -- 2.6 -- 78455 0.0 0.0 7.6
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)
1.2 1.24 72.1 0.191 -- 2.5 1.9 --

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
FOURIER SYNTHESIS 1.2 17.17 -- 0.0 -- 74518 3937 91.63 0.12185 0.12185 0.12007 0.15495 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 1.2 1.23 -- 209 4150 0.155 0.176 -- 69.16
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.122
Anisotropic B[1][1] 0.19
Anisotropic B[1][2] 0.09
Anisotropic B[1][3] 0.17
Anisotropic B[2][2] 0.23
Anisotropic B[2][3] 0.19
Anisotropic B[3][3] -0.14
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 4.208
r_sphericity_free 5.659
r_rigid_bond_restr 1.777
r_scangle_it 3.365
r_scbond_it 2.57
r_mcangle_it 1.819
r_mcbond_it 1.296
r_nbd_refined 0.211
r_gen_planes_refined 0.009
r_chiral_restr 0.1
r_dihedral_angle_4_deg 18.44
r_dihedral_angle_3_deg 12.094
r_dihedral_angle_2_deg 32.803
r_dihedral_angle_1_deg 5.773
r_angle_refined_deg 1.531
r_bond_refined_d 0.012
r_nbtor_refined 0.323
r_xyhbond_nbd_refined 0.16
r_symmetry_vdw_refined 0.171
r_symmetry_hbond_refined 0.163
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2350
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 745

Software

Computing
Computing Package Purpose
MarDB Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
MolRep Structure Solution
REFMAC 5.3.0037 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.3.0037 refinement
MolRep model building
MarDB data collection