Experiment: 9YJL

Joint X-ray/neutron structure of wild-type 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
2.48	50.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.201	α = 90
b = 67.201	β = 90
c = 60.814	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	POSITION SENSITIVE DETECTOR	ORNL ANGER CAMERA		2023-07-05	L	LAUE
2	1	x-ray	293	PIXEL	DECTRIS EIGER R 4M		2023-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SPALLATION SOURCE	ORNL Spallation Neutron Source BEAMLINE MANDI	2-4.16	ORNL Spallation Neutron Source	MANDI
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	2.48	14.7	95.5	0.201			0.096	0.95		7.6	4.6		5519
2	1.9	60.8	99.6	0.058			0.023	0.997		25	7.4		12840

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	2.48	2.57		0.233			0.131	0.295		2.8	3.6
2	1.9	1.97		0.663			0.297	0.623		1.6	5.5

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	2.48	14.7		2.5		5519	305	93.8			0.279		0.311		random	35.69
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.9	40		2.5		11690	609	90.8			0.219	0.3472	0.226	0.3435	random	35.69

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	19.5
x_torsion_deg	19.5
x_angle_deg	1.1
x_angle_deg	1.1
x_torsion_impr_deg	0.77
x_torsion_impr_deg	0.77
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	59
Heterogen Atoms	5

Software

Software
Software Name	Purpose
nCNS	refinement
Mantid	data reduction
LAUENORM	data scaling
PHASER	phasing