5C5I

Crystal structure of NADP-dependent dehydrogenase from Rhodobacter sphaeroides


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ZQB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52890.2 ul of 10.5 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 2 condition # 72 (20%w/v PEG 3350, 0.2M Li nitrate) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin
Crystal Properties
Matthews coefficientSolvent content
238.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.048α = 90
b = 80.085β = 93.69
c = 61.33γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.25096.40.0740.0740.0850.048.74.426059-341.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2479.50.5270.6020.2860.8932.23.91079

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 REPLACEMENTTHROUGHOUT4ZQB2.25026059125396.360.19730.19450.252RANDOM62.532
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]
-1.111.167.09-6.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.004
r_dihedral_angle_4_deg22.018
r_dihedral_angle_3_deg13.702
r_dihedral_angle_1_deg5.807
r_mcangle_it2.457
r_angle_refined_deg1.657
r_mcbond_other1.58
r_mcbond_it1.579
r_angle_other_deg1.271
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.004
r_dihedral_angle_4_deg22.018
r_dihedral_angle_3_deg13.702
r_dihedral_angle_1_deg5.807
r_mcangle_it2.457
r_angle_refined_deg1.657
r_mcbond_other1.58
r_mcbond_it1.579
r_angle_other_deg1.271
r_chiral_restr0.089
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4537
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms

Software

Software
Software NamePurpose
BLU-MAXdata collection
HKL-3000data reduction
HKL-3000phasing
HKL-3000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction