X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 293.0
Details 25% PEG 2000, 0.2 M MgCl2, 0.1 M Tris , 4 mM NiCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.67 α = 90
b = 81.62 β = 108.8
c = 52.1 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-11-03
Diffraction Radiation
Monochromator Protocol
Diamond (111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.933 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
1.3 28.3 95.2 0.042 0.039 -- 5.9 -- 84137 3.64 3.1 14.11
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)
1.3 1.33 84.1 0.213 0.241 3.1 2.8 4517

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 1.3 49.39 -- 3.678 88637 79880 4225 94.89 -- 0.14465 0.14313 0.17428 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 1.3 1.334 -- 257 5229 0.195 0.22 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Overall
Mean Isotropic B 9.253
Anisotropic B[1][1] -0.18
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.23
Anisotropic B[2][2] -0.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.15
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_other 0.335
r_bond_other_d 0.003
r_mcangle_it 1.875
r_angle_refined_deg 1.481
r_bond_refined_d 0.013
r_nbd_other 0.259
r_chiral_restr 0.091
r_scangle_it 3.977
r_gen_planes_refined 0.007
r_nbd_refined 0.218
r_xyhbond_nbd_refined 0.176
r_mcbond_it 1.265
r_dihedral_angle_1_deg 6.702
r_symmetry_vdw_refined 0.232
r_angle_other_deg 0.836
r_nbtor_other 0.088
r_gen_planes_other 0.003
r_symmetry_hbond_refined 0.222
r_scbond_it 2.706
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.052
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3230
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 633

Software

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