4WE3 | pdb_00004we3

STRUCTURE OF THE BINARY COMPLEX OF A ZINGIBER OFFICINALE DOUBLE BOND REDUCTASE IN COMPLEX WITH NADP MONOCLINIC CRYSTAL FORM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NH4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	PEG 1500 24%, PCB 100 mM

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.704	α = 90
b = 133.447	β = 101.39
c = 90.942	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 PILATUS 6M	mirrors	2014-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.968630	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.49	46.4	99.3	0.089	0.101	11.04	4.51	53557	53557		-3	59.919

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.49	2.58	99.1		0.998	1.125	1.74	4.61

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	4NH4	2.6	46.4	44714	2374	99.4	0.2245	0.2223	0.22	0.265	0.26	RANDOM	49.76

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]
-1.56		-4.84	-0.28		3.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.551
r_dihedral_angle_4_deg	21.083
r_dihedral_angle_3_deg	15.616
r_dihedral_angle_1_deg	5.861
r_mcangle_it	5.365
r_angle_other_deg	3.775
r_mcbond_it	3.53
r_mcbond_other	3.528
r_angle_refined_deg	1.501
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.551
r_dihedral_angle_4_deg	21.083
r_dihedral_angle_3_deg	15.616
r_dihedral_angle_1_deg	5.861
r_mcangle_it	5.365
r_angle_other_deg	3.775
r_mcbond_it	3.53
r_mcbond_other	3.528
r_angle_refined_deg	1.501
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_other	0.007
r_gen_planes_refined	0.006
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10141
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	192

Software

Software
Software Name	Purpose
XDS	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
PHASER	phasing
XSCALE	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.