6YTZ | pdb_00006ytz

Crystal structure of Malus domestica Double Bond Reductase (MdDBR) in complex with NADPH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YSB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.03 M sodium chloride, 0.03 M sodium bromide, 0.03 M sodium iodide in 0.1 M MES/imidazole pH 6.5.

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.545	α = 90
b = 68.645	β = 90
c = 145.398	γ = 90

Symmetry
Space Group	I 2 2 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	PIXEL	DECTRIS PILATUS 2M		2018-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.00	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.4	48.5	100	1	15.9	12.47		67744

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42			0.517

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	6YSB	1.4	48.44	64352	3403	99.99	0.1237	0.1215	0.1216	0.1661	0.1659	RANDOM	25.337

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]
-0.37			-0.14		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.713
r_dihedral_angle_4_deg	18.557
r_dihedral_angle_3_deg	13.991
r_dihedral_angle_1_deg	7.24
r_rigid_bond_restr	4.191
r_angle_refined_deg	1.919
r_angle_other_deg	1.519
r_chiral_restr	0.116
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2703
Nucleic Acid Atoms
Solvent Atoms	288
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction
SCALA	data scaling