3CP3

Crystal structure of conserved protein of unknown function DIP1874 from Corynebacterium diphtheriae


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.7
Temperature 295.0
Details 30% PEG 8000, 0.1 M Acetate pH 4.5, 0.2 M Lithium sulfate, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.37 α = 90
b = 59.37 β = 90
c = 98.95 γ = 90
Symmetry
Space Group I 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-3 Mirrors 2007-06-04
Diffraction Radiation
Monochromator Protocol
Double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID

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
1.98 50.9 97.3 0.049 -- -- 11.7 11597 11597 0.0 0.0 41.0
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)
1.98 2.05 76.4 0.297 -- 5.77 8.6 905

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 2.0 29.68 -- 0.0 11027 11027 549 99.46 0.19 0.19 0.188 0.229 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 2.05 827 34 793 0.208 0.223 -- 97.41
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.883
Anisotropic B[1][1] 0.52
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.52
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.05
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 16.494
r_gen_planes_refined 0.008
r_mcangle_it 2.205
r_angle_refined_deg 1.76
r_symmetry_vdw_refined 0.219
r_scbond_it 2.546
r_dihedral_angle_4_deg 26.74
r_dihedral_angle_2_deg 35.438
r_nbd_refined 0.236
r_nbtor_refined 0.312
r_xyhbond_nbd_refined 0.213
r_scangle_it 3.761
r_chiral_restr 0.129
r_mcbond_it 1.361
r_bond_refined_d 0.018
r_dihedral_angle_1_deg 7.819
r_symmetry_hbond_refined 0.163
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1028
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 78

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
SBC-Collect data collection
HKL-3000 data collection
HKL-3000 data reduction
HKL-3000 data scaling
MOLREP phasing