2V6F | pdb_00002v6f

Structure of Progesterone 5beta-Reductase from Digitalis Lanata

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6		1 MICROL OF PROTEIN SOLUTION WAS MIXED WITH 1 MICROL OF RESERVOIR SOLUTION (15 % PEG 4000, 0.1 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE, PH 5.6) AND THE DROPLET SUSPENDED OVER 700 ML OF RESERVOIR SOLUTION.

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.66	α = 90
b = 78.66	β = 90
c = 180.99	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	MAD

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	2.4	40	99.9	0.06	33.7	18.9		23196		3	62.6

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	2.4	2.56	100		0.6	5.6	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	MAD	THROUGHOUT	NONE	2.4	39.34	20737	2304	100	0.21	0.205	0.28	0.251	0.29	RANDOM	47.66

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]
5.51			5.51		-11.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.957
r_dihedral_angle_4_deg	18.55
r_dihedral_angle_3_deg	17.639
r_dihedral_angle_1_deg	7.151
r_scangle_it	2.11
r_scbond_it	1.439
r_angle_refined_deg	1.432
r_angle_other_deg	0.968
r_mcangle_it	0.955
r_mcbond_it	0.534
r_symmetry_hbond_refined	0.261
r_nbd_refined	0.209
r_nbtor_refined	0.186
r_symmetry_vdw_other	0.185
r_nbd_other	0.184
r_xyhbond_nbd_refined	0.172
r_symmetry_vdw_refined	0.108
r_nbtor_other	0.09
r_chiral_restr	0.084
r_bond_refined_d	0.014
r_bond_other_d	0.004
r_gen_planes_refined	0.004
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	2787
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	1

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement