9FM8 | pdb_00009fm8

Imine Reductase from Rhodococcus erythropolis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	0.1 M bis Tris propane pH 5.5; 0.2 M MgCl2; 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.66	α = 90
b = 80.66	β = 90
c = 82.78	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	PIXEL	DECTRIS EIGER2 XE 16M		2024-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	097627	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.38	53.44	100	0.14	0.03	1	8.6	19.8		12900			47

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.38	2.47			0.98	0.22	0.96	0.6

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 (Observed)	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	2.38	53.44	12169	705	99.96	0.22179	0.21756	0.2286	0.29968	0.3031	RANDOM	67.858

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]
3.15	1.58		3.15		-10.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.865
r_long_range_B_refined	11.776
r_long_range_B_other	11.774
r_scangle_other	9.3
r_mcangle_it	9.095
r_mcangle_other	9.092
r_dihedral_angle_2_deg	8.901
r_dihedral_angle_1_deg	7.418
r_mcbond_it	6.121
r_mcbond_other	6.12
r_scbond_it	6.033
r_scbond_other	6.03
r_angle_refined_deg	1.443
r_angle_other_deg	0.52
r_chiral_restr	0.071
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2052
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms

Software

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