9B2G | pdb_00009b2g

Crystal structure of short chain dehydrogenase reductase 9 (short chain dehydrogenase reductase 9C4) in complex with NADH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9B2F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	295	15% Jeffamine SD-2001, 0.1 M Na citrate pH 5.4

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.116	α = 90
b = 74.205	β = 133.12
c = 102.771	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 EIGER X 16M		2021-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9791	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	50	99.3	0.033	0.999	10.5	4.5		52809

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	99.1		0.426	0.809	2	4.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2	40	49599	2680	98.22	0.20334	0.20148	0.2127	0.23844	0.2472	RANDOM	74.779

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]
6.28		4.2	-9.23		-1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.886
r_dihedral_angle_4_deg	17.253
r_dihedral_angle_3_deg	16.814
r_dihedral_angle_1_deg	6.903
r_long_range_B_other	6.61
r_long_range_B_refined	6.609
r_scangle_other	5.151
r_mcangle_other	4.167
r_mcangle_it	4.166
r_scbond_it	3.239
r_scbond_other	3.239
r_mcbond_it	2.817
r_mcbond_other	2.814
r_angle_refined_deg	1.426
r_angle_other_deg	1.211
r_chiral_restr	0.06
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4599
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing