7AHW | pdb_00007ahw

The crystal structure of gene product PA4063 from Pseudomonas aeruginosa

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7ALY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	ammonium sulfate 2M, sodium chloride 2M

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.825	α = 90
b = 65.825	β = 90
c = 101.22	γ = 90

Symmetry
Space Group	P 41 21 2

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 PILATUS 6M		2019-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.000100	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.95	46.55	99.9	0.081	0.088	0.035	0.999	17.3	11.7		16839

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2			0.037	0.04	0.015	0.999		8.9

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7ALY	1.952	42.324	16788	825	99.857	0.195	0.1934	0.2	0.2202	0.22	39.707

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]
0.024			0.024		-0.048

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.393
r_dihedral_angle_4_deg	15.299
r_dihedral_angle_3_deg	15.164
r_lrange_other	10.897
r_lrange_it	10.891
r_scangle_it	9.686
r_scangle_other	9.686
r_scbond_it	6.496
r_scbond_other	6.49
r_dihedral_angle_1_deg	6.397
r_mcangle_other	4.676
r_mcangle_it	4.649
r_mcbond_it	3.681
r_mcbond_other	3.636
r_angle_refined_deg	1.835
r_angle_other_deg	1.403
r_symmetry_nbd_refined	0.308
r_nbd_refined	0.208
r_symmetry_xyhbond_nbd_refined	0.196
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.157
r_nbd_other	0.126
r_xyhbond_nbd_refined	0.119
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.087
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1002
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms

Software

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