9B2F | pdb_00009b2f

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6FFB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	295	15% Jeffamine SD-2001, 0.1 M Na citrate pH 5.0, 0.1 M Na malonate

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.384	α = 90
b = 103.045	β = 90
c = 103.082	γ = 90

Symmetry
Space Group	I 2 2 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	PIXEL	DECTRIS EIGER X 16M		2021-04-09	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	1.66	72.88	99.2	0.024	0.999	13.5	13		46581

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	1.66	1.75			0.482	0.764	1.7

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 (All)	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	1.662	50.005	46568	968	99.227	0.167	0.1661	0.1794	0.1931	0.2017	RANDOM	42.658

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]
-2.535			4.69		-2.155

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.436
r_dihedral_angle_6_deg	14.267
r_dihedral_angle_2_deg	10.722
r_lrange_it	9.636
r_lrange_other	9.632
r_scangle_it	8.078
r_scangle_other	8.075
r_dihedral_angle_1_deg	6.515
r_scbond_it	5.254
r_scbond_other	5.235
r_mcangle_other	4.897
r_mcangle_it	4.879
r_mcbond_it	3.728
r_mcbond_other	3.724
r_angle_refined_deg	1.825
r_angle_other_deg	0.6
r_nbd_refined	0.231
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.157
r_symmetry_nbd_refined	0.125
r_nbd_other	0.112
r_symmetry_xyhbond_nbd_refined	0.107
r_chiral_restr	0.086
r_symmetry_xyhbond_nbd_other	0.085
r_symmetry_nbtor_other	0.082
r_dihedral_angle_other_2_deg	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2299
Nucleic Acid Atoms
Solvent Atoms	143
Heterogen Atoms	51

Software

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