5CRF

Structure of the penicillin-binding protein PonA1 from Mycobacterium Tuberculosis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	273	0.2 M Lithium chloride, 0.1 M HEPES, 20 % PEG6000

Crystal Properties
Matthews coefficient	Solvent content
1.81	31.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.006	α = 90
b = 333.314	β = 108.37
c = 47.528	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARMOSAIC 300 mm CCD		2014-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.987857	APS	21-ID-G

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	1.8	30	96.8	0.07	30.3	4.9		120754

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	1.8	1.83	97.6		0.53	2.4	4.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.8	30	114638	6020	96.58	0.16302	0.16083	0.20523	RANDOM	31.899

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]
1.4		-0.62	-1.48		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.51
r_dihedral_angle_4_deg	15.423
r_dihedral_angle_3_deg	13.274
r_long_range_B_refined	6.232
r_long_range_B_other	6.091
r_dihedral_angle_1_deg	6.042
r_scangle_other	1.962
r_mcangle_it	1.731
r_mcangle_other	1.731
r_angle_refined_deg	1.645
r_scbond_it	1.215
r_scbond_other	1.197
r_mcbond_it	1.012
r_mcbond_other	1.011
r_angle_other_deg	0.989
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11194
Nucleic Acid Atoms
Solvent Atoms	962
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing