X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.4
Temperature 298.0
Details 0.1 M Tris, 4 mM NiCl2,40% PEG 2000, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.59 α = 90
b = 47.9 β = 99.02
c = 72.42 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Diamond --
Diffraction Radiation
Monochromator Protocol
Diamond(111), Ge(220), Toroidal mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2

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
1.6 29.88 95.7 0.098 0.083 -- 3.5 43875 43352 1.151 1.8 24.3
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)
1.6 1.69 79.8 0.366 0.292 1.8 2.7 5230

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
SAD 1.6 29.88 -- 0.0 43352 41144 2190 95.45 0.175 0.17486 0.17257 0.21679 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 1.6 1.642 2372 114 2372 0.312 0.302 0.108 79.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 18.893
Anisotropic B[1][1] 0.52
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.09
Anisotropic B[2][2] -0.88
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.33
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.625
r_gen_planes_other 0.005
r_scbond_it 2.688
r_nbd_refined 0.202
r_nbtor_other 0.089
r_xyhbond_nbd_refined 0.206
r_symmetry_vdw_other 0.244
r_angle_other_deg 0.979
r_mcangle_it 2.043
r_rigid_bond_restr 1.627
r_sphericity_bonded 2.309
r_scangle_it 3.68
r_gen_planes_refined 0.009
r_bond_refined_d 0.019
r_nbd_other 0.259
r_symmetry_hbond_refined 0.229
r_bond_other_d 0.003
r_angle_refined_deg 1.822
r_symmetry_vdw_refined 0.17
r_sphericity_free 3.516
r_chiral_restr 0.117
r_mcbond_it 1.593
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.108
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3145
Nucleic Acid Atoms 0
Heterogen Atoms 72
Solvent Atoms 507

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
SOLVE phasing
REFMAC refinement version: 5.1.19
CCP4 data scaling version: (SCALA)