3H8U

Crystal structure of uncharacterized conserved protein with double-stranded beta-helix domain (YP_001338853.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.80 A resolution


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 277.0
Details 1.7000M (NH4)2SO4, 15.0000% Glycerol, 1.7000% PEG-400, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.85 α = 90
b = 46.85 β = 90
c = 94.94 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD Adjustable focusing mirrors in K-B geometry 2008-10-12
Diffraction Radiation
Monochromator Protocol
Si(111) Double Crystal Monochrometer MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 0.94645,0.97965 APS 23-ID-B

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
1.8 24.95 96.6 0.065 -- -- 2.86 -- 21525 -- -3.0 19.864
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)
1.8 1.86 92.7 0.491 -- 1.44 -- --

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 1.8 24.953 -- 0.0 -- 21489 1044 99.74 -- 0.154 0.152 0.196 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 1.801 1.848 -- 56 1480 0.217 0.31 -- 98.34
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.881
Anisotropic B[1][1] 0.41
Anisotropic B[1][2] 0.21
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.41
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.62
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.509
r_dihedral_angle_1_deg 6.733
r_mcbond_it 0.756
r_gen_planes_refined 0.008
r_mcangle_it 1.214
r_bond_other_d 0.002
r_dihedral_angle_4_deg 8.859
r_symmetry_vdw_other 0.234
r_dihedral_angle_2_deg 31.571
r_nbd_other 0.181
r_mcbond_other 0.214
r_symmetry_hbond_refined 0.138
r_bond_refined_d 0.015
r_scangle_it 3.213
r_xyhbond_nbd_refined 0.179
r_chiral_restr 0.093
r_scbond_it 1.995
r_gen_planes_other 0.004
r_angle_other_deg 0.774
r_nbtor_refined 0.177
r_nbd_refined 0.199
r_nbtor_other 0.082
r_dihedral_angle_3_deg 11.939
r_symmetry_vdw_refined 0.127
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1776
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 207

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PHENIX refinement
SHELX phasing
REFMAC refinement version: 5.2.0005
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.006
XDS data reduction
SHELXD phasing
autoSHARP phasing