X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details WELL CONTAINED 40% PENTAERYTHRITOL PROPOXYLATE 629, 0.08M K2HPO4. DROP CONTAINED 0.002 M MNCL2, 0.002M FOSFOMYCIN, 10 MG/ML FOSA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.8 α = 90
b = 65.87 β = 90
c = 76.96 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-02-16
Diffraction Radiation
Monochromator Protocol
Si(111) double-crystal monochromator, Bent cylindrical Si-mirror (Rh coating) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-D 0.9780, 0.9789, 0.9537 APS 14-BM-D

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 30 96.0 0.07 -- -- 10.2 19809 19809 -- -3.0 27.0
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)
2.0 2.07 84.9 0.17 -- 11.0 -- --

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
MAD 2.0 30.0 -- 0.0 17952 17952 966 95.82 0.2001 0.20014 0.19741 0.25224 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 2.0 2.052 -- 62 1077 0.205 0.253 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.182
Anisotropic B[1][1] -0.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.98
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.88
r_xyhbond_nbd_refined 0.177
r_symmetry_vdw_refined 0.337
r_mcbond_it 1.117
r_scangle_it 4.545
r_nbd_other 0.22
r_xyhbond_nbd_other 0.249
r_mcangle_it 1.928
r_dihedral_angle_3_deg 13.745
r_gen_planes_refined 0.009
r_nbd_refined 0.284
r_angle_other_deg 0.88
r_chiral_restr 0.114
r_bond_refined_d 0.019
r_symmetry_vdw_other 0.307
r_bond_other_d 0.001
r_angle_refined_deg 2.342
r_gen_planes_other 0.004
r_nbtor_other 0.451
r_dihedral_angle_1_deg 4.734
r_symmetry_hbond_refined 0.327
r_symmetry_hbond_other 0.161
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2130
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 126

Software

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