7YA4

Formate dehydrogenase from Novosphingobium sp. AP12 with NAD and Azide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XYB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	PEG 3350, Tacsimate (Hampton Research, USA)

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.794	α = 90
b = 95.789	β = 99.282
c = 117.93	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 270		2021-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

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	1.8	50	97.9	0.08	24.6	3.4		143534

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	1.8	1.83			0.287

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4XYB	1.8	34.138	140486	7007	97.707	0.157	0.1552	0.1908	17.076

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]
0.855		-1.96	1.168		-1.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.154
r_dihedral_angle_3_deg	14.134
r_dihedral_angle_2_deg	10.777
r_dihedral_angle_1_deg	7.136
r_lrange_it	4.207
r_lrange_other	4.17
r_scangle_it	3.502
r_scangle_other	3.502
r_scbond_it	2.247
r_scbond_other	2.247
r_mcangle_it	1.826
r_mcangle_other	1.826
r_angle_refined_deg	1.533
r_mcbond_it	1.346
r_mcbond_other	1.338
r_angle_other_deg	0.527
r_nbd_refined	0.219
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.176
r_nbd_other	0.168
r_symmetry_nbd_refined	0.155
r_xyhbond_nbd_refined	0.129
r_symmetry_xyhbond_nbd_refined	0.115
r_chiral_restr	0.078
r_symmetry_nbtor_other	0.078
r_metal_ion_refined	0.069
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11796
Nucleic Acid Atoms
Solvent Atoms	965
Heterogen Atoms	135

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing