1SI0

Crystal Structure of Mannheimia haemolytica Ferric iron-Binding Protein A in a closed conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q35PDB ENTRY 1Q35

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5277HEPES, isopropanol, PEG 4000, glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.8456.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.67α = 90
b = 192.941β = 90
c = 43.352γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.31.00ALS5.0.3

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
11.3595.35959025085709
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.351.499.7

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1Q351.3595.359025085709452699.860.15990.159890.159130.17416RANDOM11.398
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]
0.71-0.720.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.542
r_scangle_it4.886
r_scbond_it3.03
r_mcangle_it2.44
r_mcbond_it1.534
r_angle_refined_deg1.096
r_angle_other_deg0.718
r_symmetry_vdw_other0.308
r_nbd_other0.236
r_nbd_refined0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.542
r_scangle_it4.886
r_scbond_it3.03
r_mcangle_it2.44
r_mcbond_it1.534
r_angle_refined_deg1.096
r_angle_other_deg0.718
r_symmetry_vdw_other0.308
r_nbd_other0.236
r_nbd_refined0.21
r_symmetry_vdw_refined0.167
r_xyhbond_nbd_refined0.092
r_nbtor_other0.082
r_symmetry_hbond_refined0.08
r_chiral_restr0.063
r_bond_refined_d0.006
r_metal_ion_refined0.006
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2526
Nucleic Acid Atoms
Solvent Atoms509
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
CCP4data scaling
MOLREPphasing