3ZV6 | pdb_00003zv6

CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B-356 COMPLEX WITH CO-ENZYME NAD AND PRODUCT ANALOG 4,4'-DIHYDROXYBIPHENYL

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BDB	PDB ENTRY 1BDB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				SODIUM MALONATE, PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.217	α = 90
b = 76.217	β = 90
c = 180.573	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2011-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.15	100	99.9	0.12	19.34	8.9		30090		2	38.421

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	70.19	100		0.73	2.51	8.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1BDB	2.14	70.19	28211	1509	98.61	0.18845	0.18638	0.19	0.22654	0.23	RANDOM	40.406

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]
0.12			0.12		-0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.01
r_dihedral_angle_4_deg	19.361
r_dihedral_angle_3_deg	16.238
r_dihedral_angle_1_deg	6.261
r_scangle_it	2.35
r_scbond_it	1.639
r_angle_refined_deg	1.511
r_angle_other_deg	1.052
r_mcangle_it	0.904
r_mcbond_it	0.713
r_symmetry_vdw_other	0.288
r_nbd_refined	0.202
r_nbd_other	0.199
r_symmetry_vdw_refined	0.184
r_symmetry_hbond_refined	0.182
r_nbtor_refined	0.175
r_mcbond_other	0.153
r_xyhbond_nbd_refined	0.145
r_nbtor_other	0.09
r_chiral_restr	0.089
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3976
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	102

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing