3PBC | pdb_00003pbc

Peptidase module of the peptidoglycan hydrolase RipA (Rv1477) from Mycobacterium tuberculosis at 1.38 resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	0.2 M lithium sulphate, 0.1M Tris HCl pH 8.5, 35%w/v PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.797	α = 90
b = 66.431	β = 90
c = 68.129	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315r	mirrors	2009-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9793	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.38	66.4	98.5	0.073	0.073	12.9	4.3	16683	16433	3	3	10.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.38	1.416	83.94		0.381	0.381	3	3.6	4569

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.38	66.4	3	3	32788	16433	1730	98.28	0.12227	0.11989	0.12	0.16662	0.17	RANDOM	9.664

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]
0.3			-0.06		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.804
r_dihedral_angle_4_deg	14.507
r_sphericity_free	12.302
r_dihedral_angle_3_deg	10.527
r_dihedral_angle_1_deg	6.108
r_scangle_it	5.624
r_sphericity_bonded	4.256
r_scbond_it	4.075
r_mcangle_it	2.964
r_mcbond_it	2.132
r_rigid_bond_restr	1.97
r_angle_refined_deg	1.921
r_angle_other_deg	1.064
r_mcbond_other	0.934
r_chiral_restr	0.128
r_bond_refined_d	0.023
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1543
Nucleic Acid Atoms
Solvent Atoms	264
Heterogen Atoms

Software

Software
Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling