X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 293.0
Details PEG4000, MPD, Nacacodylate, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 115.92 α = 90
b = 39.3 β = 116.19
c = 69.15 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-03-08
Diffraction Radiation
Monochromator Protocol
Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 -- ESRF ID14-1

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
1.5 62.02 99.4 0.057 -- -- 3.7 -- 43648 0.0 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)
1.5 1.58 99.4 0.283 -- 2.5 3.5 --

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 1.5 24.254 -- 0.0 40227 40227 3063 96.0 0.1472 0.14729 0.14559 0.16969 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 1.5 1.539 -- 203 2695 0.193 0.241 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.591
Anisotropic B[1][1] -0.99
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.04
Anisotropic B[2][2] -0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.14
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.003
r_symmetry_vdw_refined 0.284
r_mcbond_it 0.967
r_gen_planes_refined 0.005
r_bond_other_d 0.002
r_symmetry_hbond_refined 0.228
r_rigid_bond_restr 0.618
r_chiral_restr 0.08
r_xyhbond_nbd_refined 0.166
r_nbtor_other 0.077
r_scbond_it 2.426
r_symmetry_vdw_other 0.288
r_sphericity_bonded 2.376
r_angle_refined_deg 1.204
r_nbd_refined 0.205
r_bond_refined_d 0.009
r_angle_other_deg 0.835
r_mcangle_it 1.601
r_sphericity_free 7.6
r_scangle_it 3.699
r_dihedral_angle_1_deg 5.145
r_nbd_other 0.237
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2163
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 358

Software

Software
Software Name Purpose
DENZO data reduction
SCALA data scaling
AMoRE phasing
REFMAC refinement version: 5.1.24
CCP4 data scaling version: (SCALA)