1XVY

Crystal Structure of iron-free Serratia marcescens SfuA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XVXpdb entry 1xvx

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4273lithium chloride, PEG 6000, citric acid, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
2.1141.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.046α = 90
b = 65.392β = 111.9
c = 50.266γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU2004-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.7424.8899.227910
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.741.895.6

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 1xvx1.7446.632702626494141498.030.1650.164950.162480.20927RANDOM12.729
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]
-0.37-0.470.03-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.75
r_dihedral_angle_4_deg12.901
r_dihedral_angle_3_deg12.289
r_dihedral_angle_1_deg5.585
r_scangle_it3.437
r_scbond_it2.24
r_angle_refined_deg1.304
r_mcangle_it1.135
r_mcbond_it0.721
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.75
r_dihedral_angle_4_deg12.901
r_dihedral_angle_3_deg12.289
r_dihedral_angle_1_deg5.585
r_scangle_it3.437
r_scbond_it2.24
r_angle_refined_deg1.304
r_mcangle_it1.135
r_mcbond_it0.721
r_nbtor_refined0.301
r_symmetry_vdw_refined0.228
r_nbd_refined0.203
r_symmetry_hbond_refined0.153
r_xyhbond_nbd_refined0.117
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2334
Nucleic Acid Atoms
Solvent Atoms424
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
CCP4data scaling
MOLREPphasing