1SI1

Crystal Structure of Mannheimia haemolytica Ferric iron-Binding Protein A in an open 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 DROP8.2277PEG 3350, sodium citrate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3547.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.031α = 90
b = 48.191β = 100.92
c = 77.362γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-07-20MSINGLE 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
11.4576.7955857455606
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.451.598.7

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 1Q351.4576.75857455606295598.730.172280.17220.171240.19132RANDOM15.466
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]
0.85-0.13-0.43-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.796
r_scangle_it5.994
r_scbond_it3.698
r_mcangle_it3.344
r_mcbond_it2.227
r_angle_refined_deg1.176
r_angle_other_deg0.746
r_symmetry_vdw_refined0.275
r_symmetry_vdw_other0.268
r_nbd_other0.237
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.796
r_scangle_it5.994
r_scbond_it3.698
r_mcangle_it3.344
r_mcbond_it2.227
r_angle_refined_deg1.176
r_angle_other_deg0.746
r_symmetry_vdw_refined0.275
r_symmetry_vdw_other0.268
r_nbd_other0.237
r_nbd_refined0.21
r_symmetry_hbond_refined0.117
r_xyhbond_nbd_refined0.115
r_nbtor_other0.083
r_chiral_restr0.07
r_metal_ion_refined0.018
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2511
Nucleic Acid Atoms
Solvent Atoms434
Heterogen Atoms1

Software

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