9FJ7 | pdb_00009fj7

Nuclease NucB from Bacillus licheniformis mutant N117Q

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	protein concentration was 18 mg/ml; storage buffer: 20mM Tris pH 8.0, 100mM NaCl; reservoir solution: 0.1 M 1,6-Hexanediol 0.1 M 1-Butanol 0.1 M 1,2-Propanediol 0.1 M 2-Propanol 0.1 M 1,4-Butanediol 0.1 M 1,3-Propanediol 0.85 M Tris and Bicine pH 8.5 10.5 % v/v 2-Methyl- -2,4,-pentanediol 10.5 % PEG 1000 10.5 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.497	α = 90
b = 53.497	β = 90
c = 84.596	γ = 120

Symmetry
Space Group	P 31 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 6M		2021-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	1.25	46.33	100	0.067	0.071	0.023	0.998	22.4	9.5		39455			12

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	1.25	1.27	100		1.659	1.752	0.556	0.659	1.7	9.7

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-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	1.25	46.33	39411	2002	99.894	0.129	0.12909	0.12549	0.1281	0.16305	0.1475	Random	17.64

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]
0.032	0.016		0.032		-0.105

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.161
r_dihedral_angle_4_deg	18.674
r_dihedral_angle_3_deg	12.015
r_dihedral_angle_1_deg	6.072
r_rigid_bond_restr	4.414
r_lrange_it	3.734
r_lrange_other	3.331
r_scangle_it	3.057
r_scangle_other	3.055
r_scbond_it	2.542
r_scbond_other	2.54
r_mcangle_other	2.218
r_mcangle_it	2.217
r_angle_refined_deg	1.825
r_mcbond_it	1.792
r_mcbond_other	1.698
r_angle_other_deg	1.671
r_nbd_refined	0.234
r_symmetry_nbd_other	0.203
r_nbd_other	0.184
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.172
r_symmetry_nbd_refined	0.163
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.009
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	844
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building