9VVS | pdb_00009vvs

NAD(P)-dependent oxidoreductase from Kutzneria albida

X-RAY DIFFRACTION

---

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, HANGING DROP		279.15	0.05 M Sodium acetate: Acetic acid pH 5.4, 0.8/1.2 M NaH2PO4/K2HPO4

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.71	α = 90
b = 117.71	β = 90
c = 98.987	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	RIGAKU HyPix-3000		2025-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-X	1.54184

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.68	12.716	99.1	0.047	0.191	0.047	0.996	12.7	2	48016	24402			10.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.68	2.77	100		0.372	0.97

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	2.68	12.716	19859	1009	98.816	0.191	0.1876	0.1946	0.2477	0.2531	11.846

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]
1.097			1.097		-2.195

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.875
r_dihedral_angle_6_deg	16.024
r_dihedral_angle_2_deg	7.758
r_dihedral_angle_1_deg	6.658
r_lrange_other	5.939
r_lrange_it	5.876
r_scangle_it	3.032
r_scangle_other	3.031
r_mcangle_it	2.188
r_mcangle_other	2.188
r_scbond_it	1.752
r_scbond_other	1.752
r_angle_refined_deg	1.351
r_mcbond_it	1.238
r_mcbond_other	1.237
r_dihedral_angle_other_2_deg	1.105
r_angle_other_deg	0.444
r_nbd_refined	0.222
r_metal_ion_refined	0.205
r_symmetry_nbd_other	0.196
r_nbd_other	0.182
r_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.169
r_symmetry_nbd_refined	0.167
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.056
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4089
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	97

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
MrBUMP	phasing