2V6G | pdb_00002v6g

Structure of Progesterone 5beta-Reductase from Digitalis Lanata in complex with NADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		NADP FREE STRUCTURE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.8		CONTAINERLESS BATCH METHOD: 300 MICROL OF HIGH-DENSITY SILICON OIL WAS TRANSFERRED INTO A WELL OF A CELL CULTURE PLATE AND OVER-LAID WITH 500 MICROL OF REGULAR SILICON OIL. AT THE INTERFACE BETWEEN THE TWO LIQUIDS A DROPLET WAS DEPOSITED THAT WAS OBTAINED BY MIXING 0.4 MICROL OF H2O, 2.2 MICROL OF 5BETA-POR SOLUTION WITH NADP AND PROGESTERONE ADDED AND 1.8 MICROL OF A CRYSTALLIZATION SOLUTION CONSISTING OF 22.9 % MPD, 3.5 % PEG 8000, 0.05 M SODIUM ACETATE, 0.02 M CACL2, PH 5.8.

Crystal Properties
Matthews coefficient	Solvent content
3.3	63.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.59	α = 90
b = 78.59	β = 90
c = 178.1	γ = 90

Symmetry
Space Group	P 43 21 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	CCD	MARRESEARCH	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1		BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.3	40	99.9	0.08	26	14.3		25629		3	49.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.4	100		0.74	4.6	14.6

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	NADP FREE STRUCTURE	2.3	39.34	23072	2557	100	0.175	0.171	0.18	0.212	0.22	RANDOM	39.24

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]
-0.25			-0.25		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.328
r_dihedral_angle_3_deg	15.913
r_dihedral_angle_4_deg	14.586
r_dihedral_angle_1_deg	6.167
r_scangle_it	2.095
r_scbond_it	1.415
r_angle_refined_deg	1.343
r_angle_other_deg	0.996
r_mcangle_it	0.862
r_mcbond_it	0.473
r_symmetry_vdw_other	0.23
r_nbd_refined	0.201
r_nbtor_refined	0.182
r_nbd_other	0.181
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.141
r_symmetry_hbond_refined	0.129
r_symmetry_vdw_refined	0.116
r_nbtor_other	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2889
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling