X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details PROTEIN WAS CONCENTRATED TO 20 MG/ML IN WATER. CRYSTALLISATION IN 200MM CALCIUM ACETATE IN 100MM HEPES BUFFER AT PH 7.0. PRECIPITANT WAS 18% POLYETHYLENE GLYCOL 8000.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.5 α = 90
b = 60.15 β = 90
c = 97.21 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1999-10-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B -- 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
1.5 20 99.5 0.07 -- -- 3.7 -- 54127 -- 0.0 --
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)
1.5 1.55 95.0 0.358 -- 3.4 3.5 --

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 1.5 20.0 -- -- -- 51648 2710 99.4 -- 0.115 0.113 0.149 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 1.5 1.54 -- 175 3475 0.144 0.182 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 8.34
Anisotropic B[1][1] -0.42
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.08
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.225
r_dihedral_angle_2_deg 40.135
r_angle_refined_deg 1.704
r_scbond_it 2.489
r_chiral_restr 0.108
r_bond_refined_d 0.015
r_symmetry_vdw_other 0.229
r_metal_ion_refined 0.137
r_gen_planes_refined 0.009
r_bond_other_d 0.002
r_xyhbond_nbd_refined 0.134
r_dihedral_angle_4_deg 19.858
r_nbd_other 0.275
r_dihedral_angle_3_deg 11.815
r_nbtor_other 0.082
r_symmetry_vdw_refined 0.129
r_angle_other_deg 1.357
r_mcangle_it 1.759
r_gen_planes_other 0.003
r_symmetry_hbond_refined 0.127
r_scangle_it 3.609
r_dihedral_angle_1_deg 5.674
r_mcbond_it 1.205
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2839
Nucleic Acid Atoms 0
Heterogen Atoms 57
Solvent Atoms 465

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.06
DENZO data reduction
SCALEPACK data scaling