Experiment: 9YJM

Joint X-ray/neutron structure of D132N Bacillus halodurans RNase H1 in the apo-form

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	291	0.1 M NaOAc pH 5.0, 0.2 M (NH4)2SO4, and 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.417	α = 90
b = 67.417	β = 90
c = 60.798	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	neutron	293	IMAGE PLATE	MAATEL IMAGINE		2024-02-28	L	LAUE
2	1	x-ray	293	PIXEL	DECTRIS EIGER R 4M		2024-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	NUCLEAR REACTOR	ORNL High Flux Isotope Reactor BEAMLINE CG4D	2.8-4.5	ORNL High Flux Isotope Reactor	CG4D
2	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	2.4	41.74	81.3	0.143			0.056	0.968		5.7	5.6		5059
2	2.2	60.8	95	0.14			0.076	0.984		8.3	4.3		8440

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.53		0.326			0.156	0.736		2.4	4
2	2.2	2.28		0.663			0.355	0.554		1.2	4.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	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
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.4	40		2.5		4337	219	68.4			0.241		0.256			35.84
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2.2	40		2.5		6765	338	80.4			0.204	0.3334	0.234	0.3448	random	35.84

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_torsion_deg	23.8
x_torsion_deg	23.8
x_angle_deg	1
x_angle_deg	1
x_torsion_impr_deg	0.75
x_torsion_impr_deg	0.75
x_bond_d	0.008
x_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1092
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	5

Software

Software
Software Name	Purpose
LAUEGEN	data reduction
SCALA	data scaling
PHASER	phasing
nCNS	refinement