4NPA

Scrystal structure of protein with unknown function from Vibrio cholerae at P22121 spacegroup


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PMB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293500mM NaCl, 10mM HEPES, 4%(v/v) Tacsimate, 18%(w/v) PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.346.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.33α = 90
b = 96.34β = 90
c = 333.26γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR225HE2010-12-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.8SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.130100111393111393-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.141001.93.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2PMB2.129.74110924105372555199.950.209410.206350.26674RANDOM33.972
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.31-0.07-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.43
r_dihedral_angle_4_deg22.183
r_dihedral_angle_3_deg17.542
r_long_range_B_refined7.417
r_dihedral_angle_1_deg7.232
r_mcangle_it5.243
r_scbond_it4.473
r_mcbond_it3.875
r_angle_refined_deg2.234
r_chiral_restr0.158
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.43
r_dihedral_angle_4_deg22.183
r_dihedral_angle_3_deg17.542
r_long_range_B_refined7.417
r_dihedral_angle_1_deg7.232
r_mcangle_it5.243
r_scbond_it4.473
r_mcbond_it3.875
r_angle_refined_deg2.234
r_chiral_restr0.158
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12536
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms27

Software

Software
Software NamePurpose
HKL-2000data collection
BALBESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling