8HMO

Crystal Structure of metal-dependent hydrolase complexed with manganese from Bacillus smithii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R61

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	293	35% 2-ethoxyethanol, 0.1 M Na/K phosphate buffer pH 6.2, 0.2 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.21	α = 90
b = 70.198	β = 105.77
c = 104.839	γ = 90

Symmetry
Space Group	P 1 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	100	PIXEL	DECTRIS PILATUS 2M		2022-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.9800	Photon Factory	BL-17A

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	2.53	44.91	97.3	0.101	0.121	0.066	0.952	8.2	3.3		41332

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.53	2.63	99.9		0.549	0.649	0.343	0.745	2.2	3.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.53	43.45	39259	2065	97.34	0.2528	0.2503	0.2987	RANDOM	57.175

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]
-0.08		0.09	0.02		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.328
r_dihedral_angle_3_deg	24.504
r_dihedral_angle_4_deg	19.619
r_long_range_B_refined	10.846
r_long_range_B_other	10.829
r_dihedral_angle_1_deg	6.836
r_scangle_other	5.286
r_mcangle_other	5.134
r_mcangle_it	5.133
r_scbond_it	3.168
r_scbond_other	3.168
r_mcbond_it	3.162
r_mcbond_other	3.157
r_angle_refined_deg	1.492
r_angle_other_deg	1.249
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002
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	9573
Nucleic Acid Atoms
Solvent Atoms	329
Heterogen Atoms	12

Software

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