X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 291.0
Details 100 mM Tris, 20% PEG MME 2000, 10 mM NiCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 131.66 α = 90
b = 78.04 β = 113.02
c = 60.31 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
IMAGE PLATE MARRESEARCH -- 2005-01-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 1.5418 -- --

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
2.2 39 99.5 -- 0.106 -- 3.7 27505 27505 0.0 0.0 36.3
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)
2.2 2.35 96.6 -- -- 2.1 3.4 --

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 2.23 39.0 -- 0.0 27505 27505 1408 99.48 0.186 0.186 0.183 0.246 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 2.226 2.284 1899 83 1816 0.254 0.337 -- 93.55
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.373
Anisotropic B[1][1] -1.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.43
Anisotropic B[2][2] 0.31
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.05
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.326
r_mcbond_other 0.13
r_chiral_restr 0.079
r_bond_refined_d 0.012
r_bond_other_d 0.001
r_nbd_other 0.18
r_scangle_it 2.342
r_nbtor_other 0.084
r_metal_ion_refined 0.2
r_angle_other_deg 0.824
r_symmetry_hbond_refined 0.205
r_dihedral_angle_3_deg 14.863
r_nbtor_refined 0.182
r_gen_planes_refined 0.005
r_xyhbond_nbd_refined 0.181
r_mcangle_it 1.006
r_scbond_it 1.574
r_dihedral_angle_1_deg 6.826
r_nbd_refined 0.218
r_mcbond_it 0.871
r_dihedral_angle_4_deg 14.442
r_gen_planes_other 0.001
r_symmetry_vdw_other 0.293
r_dihedral_angle_2_deg 33.344
r_symmetry_vdw_refined 0.192
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3616
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 232

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 1.701
MOSFLM data reduction
CCP4 data scaling version: (SCALA)
MOLREP phasing