X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.6
Details PROTEIN WAS CONCENTRATED TO 20 MG/ML IN WATER. CRYSTALLISATION IN 100MM MAGNESIUM ACETATE, 100MM ACETATE BUFFER AT PH 4.6. PRECIPITANT WAS 21% POLYETHYLENE GLYCOL 5000MME AND 5% DIMETHYLFORMAMIDE AS ADDITIVE.THE PROTEIN WAS INCUBATED WITH 1MM OF THE INHIBITOR PRIOR CRYSTALLISATION FOR AT LEAST 1 HOUR.

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
1.1 20 96.0 0.053 -- -- 4.3 -- 120133 -- 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)
1.1 1.13 91.5 0.242 -- 5.6 4.3 --

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 1.11 20.0 -- -- -- 120318 6359 94.5 -- 0.106 0.105 0.124 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 1.11 1.14 -- 400 7886 0.116 0.14 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 8.57
Anisotropic B[1][1] -0.31
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.28
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.03
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.163
r_symmetry_vdw_other 0.253
r_nbtor_other 0.085
r_mcbond_it 1.269
r_angle_refined_deg 1.907
r_angle_other_deg 1.861
r_xyhbond_nbd_refined 0.129
r_gen_planes_refined 0.011
r_bond_other_d 0.002
r_dihedral_angle_3_deg 10.94
r_symmetry_hbond_refined 0.139
r_mcangle_it 1.822
r_dihedral_angle_4_deg 19.962
r_nbd_refined 0.234
r_scbond_it 2.494
r_dihedral_angle_1_deg 6.232
r_dihedral_angle_2_deg 40.071
r_scangle_it 3.434
r_gen_planes_other 0.004
r_chiral_restr 0.122
r_bond_refined_d 0.017
r_nbd_other 0.274
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2839
Nucleic Acid Atoms 0
Heterogen Atoms 98
Solvent Atoms 603

Software

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