4NH4 | pdb_00004nh4

Structure of the binary complex of a zingiber officinale double bond reductase in complex with NADP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4MKR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	21% PEG 1450, 100mM PCB, 3mM NaN3, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.66	α = 90
b = 78.406	β = 90
c = 155.706	γ = 90

Symmetry
Space Group	P 21 21 21

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	PT COATED SI MIRRORS	2013-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87260	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.1	78.037	99.3	0.091	12.8	4.5	43868	43868		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.21	99.9		0.745	0.745	0.843	0.389	0.9	4.6	6310

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	4MKR	2.1	55.31	43787	43787	2250	99.07	0.1964	0.1964	0.193	0.2	0.2598	0.26	RANDOM	39.061

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]
0.01			0.45		-0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.737
r_dihedral_angle_3_deg	14.688
r_dihedral_angle_4_deg	12.697
r_dihedral_angle_1_deg	7.032
r_mcangle_it	3.152
r_mcbond_it	2.13
r_mcbond_other	2.13
r_angle_refined_deg	1.815
r_angle_other_deg	0.848
r_chiral_restr	0.099

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.737
r_dihedral_angle_3_deg	14.688
r_dihedral_angle_4_deg	12.697
r_dihedral_angle_1_deg	7.032
r_mcangle_it	3.152
r_mcbond_it	2.13
r_mcbond_other	2.13
r_angle_refined_deg	1.815
r_angle_other_deg	0.848
r_chiral_restr	0.099
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5391
Nucleic Acid Atoms
Solvent Atoms	337
Heterogen Atoms	96

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.