X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details TAKE 2 - 10 MG/ML PROTEIN IN 20MM MOPS,50MM NACL, 2% TREHALOSE, PH 7.5, ADD EQUAL VOLUME OF 70% MPD,0.1M PHOSPHATE BUFFER PH 7.0 IN A HANGING DROP EXPERIMENT AT 4 DEGREES CENTIGRADE.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.87 α = 90
b = 90.51 β = 90
c = 97.23 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 -- EMBL/DESY, Hamburg X31

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 30 99.2 0.039 -- -- 4.0 -- 111031 -- 2.0 --
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)
1.3 1.35 99.3 0.326 -- 3.56 3.0 --

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
OTHER 1.3 65.94 -- -- -- 104515 5505 99.2 -- 0.12 0.119 0.146 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 1.33 -- 423 7639 0.166 0.192 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.65
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.09
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.022
r_xyhbond_nbd_other 0.279
r_mcbond_it 1.521
r_symmetry_vdw_other 0.257
r_scbond_it 3.085
r_angle_other_deg 1.662
r_nbd_refined 0.404
r_gen_planes_refined 0.011
r_dihedral_angle_3_deg 14.36
r_scangle_it 4.257
r_symmetry_hbond_refined 0.527
r_gen_planes_other 0.004
r_bond_other_d 0.002
r_nbtor_other 0.93
r_symmetry_vdw_refined 0.251
r_dihedral_angle_1_deg 5.67
r_nbd_other 0.251
r_mcangle_it 2.198
r_angle_refined_deg 1.811
r_chiral_restr 0.133
r_xyhbond_nbd_refined 0.171
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3199
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 432

Software

Software
Software Name Purpose
REFMAC refinement version: 5.0
DENZO data reduction
SCALEPACK data scaling
CNS phasing