7OB7 | pdb_00007ob7

CPR-C4 - novel protease from the Candidate Phyla Radiation (CPR)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OB6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	sodium malonate dibasic monohydrate

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.307	α = 90
b = 79.731	β = 90
c = 126.196	γ = 90

Symmetry
Space Group	I 2 2 2

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 PILATUS3 6M		2019-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	1.2819	Diamond	I24

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	2.581	67.405	98.9	0.505	0.562	0.243	0.968	6.8	9.7		9190

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	2.581	2.69			7.895	8.889	3.982	0.181		8.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	7OB6	2.682	67.405	8193	398	98.747	0.236	0.2348	0.24	0.2506	0.26	49.032

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]
-1.94			6.08		-4.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.876
r_dihedral_angle_4_deg	19.829
r_lrange_it	14.438
r_dihedral_angle_3_deg	14.335
r_scangle_it	8.816
r_dihedral_angle_1_deg	7.331
r_mcangle_it	5.989
r_scbond_it	5.74
r_mcbond_it	3.833
r_angle_refined_deg	1.406
r_symmetry_nbd_refined	0.304
r_nbtor_refined	0.296
r_ext_dist_refined_d	0.223
r_nbd_refined	0.195
r_symmetry_xyhbond_nbd_refined	0.194
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.093
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1653
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
pointless	data scaling
PHASER	phasing