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_angle_refined_deg 1.822
r_dihedral_angle_1_deg 6.625
r_nbd_refined 0.202
r_nbd_other 0.259
r_symmetry_vdw_refined 0.17
r_scangle_it 3.68
r_sphericity_bonded 2.309
r_mcangle_it 2.043
r_chiral_restr 0.117
r_gen_planes_refined 0.009
r_angle_other_deg 0.979
r_mcbond_it 1.593
r_rigid_bond_restr 1.627
r_bond_other_d 0.003
r_gen_planes_other 0.005
r_sphericity_free 3.516
r_nbtor_other 0.089
r_symmetry_vdw_other 0.244
r_symmetry_hbond_refined 0.229
r_scbond_it 2.688
r_bond_refined_d 0.019
r_xyhbond_nbd_refined 0.206
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

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
SCALA data reduction
REFMAC version: 5.1.19 refinement
SOLVE model building
MOSFLM data collection