X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.6
Details PROTEIN CONCENTRATION 20MG/ML, 2M AMMONIUM SULPHATE, 25% GLYCEROL AS CRYOPROTECTANT, pH 4.60

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.35 α = 90
b = 69.57 β = 90
c = 77.09 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
1.15 40 99.6 0.054 -- -- 4.4 -- 103556 -- -- --
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)
1.15 1.19 99.7 0.36 -- 4.3 3.7 --

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 1.15 40.0 -- -- -- 98396 5206 99.3 -- 0.118 0.117 0.136 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 1.15 1.18 -- 372 7206 0.174 0.174 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.44
Anisotropic B[1][1] 1.38
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.78
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.59
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.083
r_angle_other_deg 2.066
r_rigid_bond_restr 1.645
r_gen_planes_refined 0.011
r_symmetry_vdw_refined 0.157
r_sphericity_free 5.534
r_chiral_restr 0.118
r_scbond_it 2.794
r_gen_planes_other 0.007
r_bond_refined_d 0.016
r_nbd_other 0.269
r_mcangle_it 2.222
r_xyhbond_nbd_refined 0.144
r_dihedral_angle_1_deg 6.419
r_mcbond_it 1.543
r_angle_refined_deg 1.765
r_scangle_it 4.02
r_sphericity_bonded 3.991
r_bond_other_d 0.001
r_symmetry_hbond_refined 0.192
r_nbd_refined 0.22
r_symmetry_vdw_other 0.326
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2377
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 378

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling
CCP4 phasing