9VW7 | pdb_00009vw7

NAD(P)-dependent oxidoreductase from Kutzneria albida

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8JKU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		279.15	1.0 M Ammonium Sulfate, 0.1 M HEPES:NaOH pH 7.0, and 0.5% (w/v) PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.395	α = 90
b = 117.395	β = 90
c = 99.569	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	PIXEL	DECTRIS PILATUS 6M		2025-01-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.979	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.499	45.84	98.9	0.057	0.995	13.3	1.9		24403

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.499	2.59			0.813

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.499	41.54	24401	1270	98.854	0.164	0.1603	0.1681	0.2275	0.2282	37.351

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]
-0.005			-0.005		0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.312
r_dihedral_angle_3_deg	15.974
r_lrange_other	9.015
r_lrange_it	8.992
r_dihedral_angle_2_deg	8.065
r_scangle_it	7.751
r_scangle_other	7.632
r_dihedral_angle_1_deg	6.598
r_mcangle_it	5.504
r_mcangle_other	5.504
r_scbond_it	5.14
r_scbond_other	5.068
r_mcbond_it	3.874
r_mcbond_other	3.873
r_angle_refined_deg	1.552
r_dihedral_angle_other_2_deg	0.793
r_angle_other_deg	0.508
r_nbd_refined	0.237
r_symmetry_nbd_other	0.198
r_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.182
r_nbd_other	0.172
r_symmetry_nbd_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.129
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.065
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4086
Nucleic Acid Atoms
Solvent Atoms	302
Heterogen Atoms	132

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
Aimless	data scaling
MrBUMP	phasing