5Y2W

Structure of Synechocystis PCC6803 CcmR regulatory domain in complex with 2-PG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5Y2V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52890.2 M MgCl2, 0.1 M HEPES, pH 7.5, 30% (v/v) Polyethylene glycol 400, 5 mM 2-PG
Crystal Properties
Matthews coefficientSolvent content
2.3347.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.965α = 90
b = 58.965β = 90
c = 123.958γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.97861SSRFBL17U1

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
12.25098.711.44.813083
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2899.13.35

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5Y2V2.247.261243264398.850.203080.20060.25476RANDOM52.827
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]
0.020.020.02-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.192
r_dihedral_angle_3_deg14.689
r_dihedral_angle_4_deg13.914
r_long_range_B_other9.44
r_long_range_B_refined9.436
r_scangle_other7.496
r_dihedral_angle_1_deg6.959
r_mcangle_it5.683
r_mcangle_other5.681
r_scbond_it5.026
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.192
r_dihedral_angle_3_deg14.689
r_dihedral_angle_4_deg13.914
r_long_range_B_other9.44
r_long_range_B_refined9.436
r_scangle_other7.496
r_dihedral_angle_1_deg6.959
r_mcangle_it5.683
r_mcangle_other5.681
r_scbond_it5.026
r_scbond_other4.992
r_mcbond_it4.152
r_mcbond_other4.142
r_angle_refined_deg1.743
r_angle_other_deg0.822
r_chiral_restr0.096
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1661
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms9

Software

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