6YSB | pdb_00006ysb

Crystal structure of Malus domestica Double Bond Reductase (MdDBR) apo form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J3H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		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
2.24	45.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.609	α = 90
b = 68.666	β = 111.38
c = 68.944	γ = 90

Symmetry
Space Group	C 1 2 1

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 PILATUS3 S 2M		2018-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.0	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	1.2	48.72	99.4	0.998	12.1	3.6		210636

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	1.2	1.22			0.784

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2J3H	1.2	48.62	200156	10528	99.37	0.1633	0.1615	0.1975	0.2261	RANDOM	24.003

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]
0.36		0.72	-0.91		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.243
r_dihedral_angle_4_deg	16.291
r_dihedral_angle_3_deg	13.702
r_rigid_bond_restr	11.434
r_dihedral_angle_1_deg	7.018
r_angle_refined_deg	2.126
r_angle_other_deg	1.601
r_chiral_restr	0.123
r_bond_refined_d	0.018
r_gen_planes_refined	0.013
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5261
Nucleic Acid Atoms
Solvent Atoms	527
Heterogen Atoms	10

Software

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