4QD3 | pdb_00004qd3

Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa with 5-azacytidine at 1.89 Angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JC4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	PEG 4000, Isopropanol, HEPES buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.111	α = 90
b = 64.111	β = 90
c = 156.62	γ = 120

Symmetry
Space Group	P 61 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	77	CCD	MARRESEARCH	Mirror	2013-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.89	32.08	99.9	0.075	51.7		16071	16071

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.89	1.92	99.9		0.491	4.5

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 (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	4JC4	1.89	32.08	15212	799	99.93	0.18897	0.18642	0.19	0.23803	0.25	RANDOM	28.774

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]
0.4	0.4		0.4		-1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.703
r_dihedral_angle_4_deg	14.817
r_dihedral_angle_3_deg	14.332
r_long_range_B_refined	5.59
r_long_range_B_other	5.586
r_dihedral_angle_1_deg	4.884
r_angle_other_deg	3.648
r_scangle_other	2.577
r_mcangle_other	2.05
r_mcangle_it	2.049
r_scbond_it	1.55
r_scbond_other	1.544
r_angle_refined_deg	1.305
r_mcbond_it	1.226
r_mcbond_other	1.222
r_chiral_restr	0.109
r_bond_refined_d	0.014
r_gen_planes_other	0.006
r_gen_planes_refined	0.005
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1467
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	23

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling