9Y1L | pdb_00009y1l

Crystal Structure of Putative Restriction Endonuclease Domain-Containing Protein from Leptospirillum ferriphilum YSK

X-RAY DIFFRACTION

---

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, SITTING DROP		295	Unknown

Crystal Properties
Matthews coefficient	Solvent content
1.86	33.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.989	α = 90
b = 76.989	β = 90
c = 45.84	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	SBC-3		2010-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97931	APS	19-BM

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	1.65	50	98.8	0.061	0.067	0.026	0.996	31.7	6.2		36195			22.5

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	1.65	1.68	85.9		0.295	0.322	0.15	0.912	5.7	4.4

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.65	26.961	36102	1725	98.575	0.156	0.1544	0.1581	0.1775	0.185	30.315

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]
-5.363			-5.363		10.726

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	18.797
r_dihedral_angle_3_deg	12.461
r_lrange_other	10.931
r_lrange_it	10.921
r_scangle_it	9.472
r_scangle_other	9.469
r_mcangle_it	8.427
r_mcangle_other	8.424
r_rigid_bond_restr	8.101
r_scbond_it	7.44
r_scbond_other	7.437
r_mcbond_it	6.583
r_mcbond_other	6.578
r_dihedral_angle_1_deg	5.159
r_dihedral_angle_2_deg	2.061
r_angle_refined_deg	1.488
r_angle_other_deg	0.725
r_nbd_other	0.258
r_symmetry_nbd_other	0.22
r_nbd_refined	0.199
r_nbtor_refined	0.179
r_metal_ion_refined	0.119
r_symmetry_xyhbond_nbd_refined	0.117
r_symmetry_nbd_refined	0.087
r_symmetry_nbtor_other	0.082
r_xyhbond_nbd_refined	0.082
r_chiral_restr	0.069
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2392
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing