X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.7
Temperature 278.0
Details Protein solution (5mcl): 14.5mg/ml TvNiR, 0.005M Tris borate (pH8.7). Reservoir solution (5mcl): 0.2M tri-sodium citrate dihydrate, 0.1M Tris hydrochloride (pH8.5), 30% v/v PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 193.79 α = 90
b = 193.79 β = 90
c = 193.79 γ = 90
Symmetry
Space Group P 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2004-11-05
Diffraction Radiation
Monochromator Protocol
Si(111), horizontally focusing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.843 EMBL/DESY, Hamburg BW7B

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
1.4 12 99.7 0.055 -- -- -- 469642 468027 -- -- --
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)
1.4 1.42 100.0 0.547 -- 2.7 -- --

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 1.4 12.0 -- -- -- 443992 23479 99.38 -- 0.12663 0.12595 0.13946 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 1.4 1.436 -- 1754 32925 0.16 0.18 -- 99.99
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.514
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.358
r_gen_planes_refined 0.016
r_bond_other_d 0.002
r_dihedral_angle_4_deg 16.213
r_nbtor_refined 0.207
r_angle_other_deg 0.973
r_xyhbond_nbd_refined 0.112
r_nbd_refined 0.22
r_dihedral_angle_2_deg 36.27
r_mcbond_it 1.232
r_dihedral_angle_1_deg 5.954
r_sphericity_free 7.641
r_chiral_restr 0.095
r_mcangle_it 1.821
r_nbtor_other 0.112
r_dihedral_angle_3_deg 12.076
r_symmetry_vdw_other 0.327
r_symmetry_metal_ion_refined 0.15
r_metal_ion_refined 0.116
r_angle_refined_deg 1.558
r_sphericity_bonded 3.834
r_scbond_it 2.445
r_bond_refined_d 0.018
r_symmetry_vdw_refined 0.18
r_rigid_bond_restr 1.385
r_mcbond_other 0.708
r_nbd_other 0.214
r_gen_planes_other 0.001
r_symmetry_hbond_refined 0.123
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.141
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8217
Nucleic Acid Atoms 0
Heterogen Atoms 922
Solvent Atoms 1385

Software

Software
Software Name Purpose
HKL-2000 data collection
REFMAC refinement version: 5.2.0019
DENZO data reduction
SCALEPACK data scaling