3ZV3 | pdb_00003zv3

CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE (BPHB)FROM PANDORAEA PNOMENUSA STRAIN B-356 IN INTERMEDIATE STATE OF SUBSTRATE BINDING LOOP

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
2.21	44.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.735	α = 90
b = 75.735	β = 90
c = 178.947	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	IMAGE PLATE	MAR scanner 345 mm plate	MIRROR	2010-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER

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	2.8	100	98.9	0.15	7.44	4.8		13445		2	70.134

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	2.9	69.67	98.3		0.85	1.08	3.5

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	2.9	69.67	11486	601	99.08	0.26917	0.26788	0.27	0.2946	0.3	RANDOM	49.376

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]
-2.11			-2.11		4.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.058
r_dihedral_angle_3_deg	16.854
r_dihedral_angle_4_deg	15.913
r_dihedral_angle_1_deg	5.451
r_angle_refined_deg	0.999
r_angle_other_deg	0.867
r_symmetry_hbond_refined	0.261
r_symmetry_vdw_other	0.22
r_nbd_other	0.202
r_nbd_refined	0.194
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.163
r_symmetry_vdw_refined	0.124
r_nbtor_other	0.084
r_chiral_restr	0.051
r_xyhbond_nbd_other	0.033
r_bond_refined_d	0.007
r_bond_other_d	0.006
r_gen_planes_refined	0.002
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	3916
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms

Software

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