8ZKD | pdb_00008zkd

The Crystal Structure of the RON from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PLS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	20% PEG 2000

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.193	α = 90
b = 98.193	β = 90
c = 46.873	γ = 90

Symmetry
Space Group	P 41

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 EIGER X 9M		2024-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.952998	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.05	49.1	100	0.067	20.2	13.8		28370

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.11			0.769

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	2.05	49.1	28348	1457	99.972	0.18	0.1774	0.19	0.2305	0.24	54.292

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]
-4.085			-4.085		8.171

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.033
r_dihedral_angle_3_deg	12.4
r_lrange_it	8.989
r_lrange_other	8.953
r_scangle_it	6.909
r_scangle_other	6.907
r_dihedral_angle_1_deg	6.35
r_dihedral_angle_2_deg	6.019
r_mcangle_it	5.146
r_mcangle_other	5.145
r_scbond_it	4.465
r_scbond_other	4.465
r_mcbond_it	3.525
r_mcbond_other	3.516
r_angle_refined_deg	1.323
r_angle_other_deg	0.477
r_symmetry_xyhbond_nbd_refined	0.268
r_symmetry_nbd_refined	0.229
r_nbd_refined	0.215
r_symmetry_nbd_other	0.193
r_nbd_other	0.191
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.164
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.067
r_chiral_restr_other	0.042
r_dihedral_angle_other_2_deg	0.012
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2411
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing