6UYK | pdb_00006uyk

Dark-operative protochlorophyllide oxidoreductase in the nucleotide-free form.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FWY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		288	1 ul BchL protein in 100 mM HEPES pH 7.5, 150 mM NaCl, 10% (v/v) glycerol was mixed with 2 ul well solution containing 0.6 M sodium chloride, 0.1 M MES:NaOH pH 6.5, 20% (w/v) PEG 4000. Prior to freezing, the well solution was mixed in an equal volume of cryoprotectant solution with a final concentration of 9% (w/v) sucrose, 2% (w/v) glucose, 8% (v/v) glycerol, and 8% (v/v) ethylene glycol. Crystals were soaked for a few seconds in the cryoprotectant before being frozen in liquid nitrogen

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.513	α = 90
b = 100.918	β = 99.27
c = 117.789	γ = 90

Symmetry
Space Group	I 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 EIGER X 9M		2018-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	1.008	NSLS-II	17-ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.6	42.2	99.5	0.173	0.057	0.99	9.2	9.3		32733			80.66

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.69	95.3		0.908	0.413	0.573	1.5	5.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3FWY	2.6	41.71	1.34	32732	2873	99.41	0.2354	0.2314	0.2772	85.6

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.0058
f_angle_d	0.393
f_chiral_restr	0.0398
f_plane_restr	0.0034
f_bond_d	0.0019

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7648
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	18

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

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.