9QGC | pdb_00009qgc

Crystal structure of an NADH-accepting ene reductase variant NostocER1-L1,5 mutant Q204K

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		293	25 mM sodium phosphate pH 7.2, 75 mM NaCl, 25 mM Tris-HCl pH 8.5, 0.1 M NH4Cl, 5 mM CaCl2, 15% (w/v) PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.36	α = 90
b = 68.56	β = 90
c = 90.04	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER2 X 16M		2023-08-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.239	50	99.5	0.999	15.05	9.31		97454

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	1.24	1.31	97		0.522	1.32	6.66

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	1.239	47.159	97454	4873	99.465	0.131	0.1289	0.1288	0.1633	0.1632	18.414

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]
-0.894			-0.898		1.792

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.584
r_lrange_it	13.104
r_dihedral_angle_3_deg	12.232
r_dihedral_angle_2_deg	11.024
r_scangle_it	8.395
r_dihedral_angle_1_deg	6.339
r_scbond_it	6.155
r_mcangle_it	5.572
r_rigid_bond_restr	4.927
r_mcbond_it	4.011
r_angle_refined_deg	1.922
r_nbtor_refined	0.318
r_symmetry_nbd_refined	0.247
r_symmetry_xyhbond_nbd_refined	0.212
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.186
r_chiral_restr	0.12
r_gen_planes_refined	0.015
r_bond_refined_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2745
Nucleic Acid Atoms
Solvent Atoms	467
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing