10RY | pdb_000010ry

Crystal structure of compound 8t bound to PaLpxC

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5UPG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	100 mM Tris pH 7.4, 32% PEG Smear Medium, 2% glycerol, 2 mM TCEP

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.745	α = 90
b = 108.745	β = 90
c = 58.261	γ = 120

Symmetry
Space Group	P 63

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	APEX II CCD		2020-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5406

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.9	36.62	100	0.999	12.2	1.9		31043

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.902	1.951	98.7		1		1.8

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	1.902	35.621	31026	1606	99.942	0.2	0.1979	0.2006	0.2299	0.2376	31.624

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]
0.532	0.266		0.532		-1.725

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.939
r_dihedral_angle_3_deg	13.609
r_dihedral_angle_2_deg	9.806
r_lrange_it	8.989
r_lrange_other	8.985
r_dihedral_angle_1_deg	7.035
r_scangle_other	6.551
r_scangle_it	6.546
r_mcangle_it	4.646
r_mcangle_other	4.644
r_scbond_it	4.252
r_scbond_other	4.246
r_mcbond_it	3.049
r_mcbond_other	3.048
r_angle_refined_deg	1.763
r_angle_other_deg	0.598
r_symmetry_xyhbond_nbd_refined	0.215
r_nbd_refined	0.204
r_symmetry_nbd_refined	0.198
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.168
r_nbd_other	0.141
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2348
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement