2FT6

Structure of Cu(II)azurin with the metal-binding loop sequence "CTFPGHSALM" replaced with "CTPHPM"


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AZUPDB ENTRY 4AZU, Chain A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62930.1MM MES, 20% PEG6000, 0.2M LiCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8634.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.788α = 90
b = 51.788β = 90
c = 75.553γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.11.075SRSPX10.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
11.2532.95399.90.060.065.810291762917611.35
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.251.3299.70.2910.2916.19.24155

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 4AZU, Chain A1.2532.952911729117148899.870.1290.1290.1270.155RANDOM10.608
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]
-0.35-0.350.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.112
r_dihedral_angle_4_deg16.03
r_sphericity_free11.137
r_dihedral_angle_3_deg10.233
r_sphericity_bonded6.964
r_dihedral_angle_1_deg6.563
r_scangle_it4.55
r_scbond_it3.594
r_mcangle_it2.735
r_mcbond_it2.034
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.112
r_dihedral_angle_4_deg16.03
r_sphericity_free11.137
r_dihedral_angle_3_deg10.233
r_sphericity_bonded6.964
r_dihedral_angle_1_deg6.563
r_scangle_it4.55
r_scbond_it3.594
r_mcangle_it2.735
r_mcbond_it2.034
r_angle_refined_deg1.748
r_rigid_bond_restr1.675
r_mcbond_other1.115
r_angle_other_deg0.897
r_symmetry_vdw_refined0.311
r_symmetry_vdw_other0.299
r_symmetry_hbond_refined0.231
r_nbd_refined0.228
r_xyhbond_nbd_refined0.19
r_nbd_other0.183
r_nbtor_refined0.173
r_chiral_restr0.121
r_nbtor_other0.088
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms944
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms1

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
AMoREphasing