7AMX

The crystal structure of gene product PA4063 from Pseudomonas aeruginosa in complex with zinc

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294	ammonium sulfate 2.3M, NaCl 2.1M

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.467	α = 90
b = 62.467	β = 90
c = 102.076	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 EIGER2 X 4M		2020-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.96770	ESRF	ID30B

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	2.85	62.47	99.6	0.203	0.212	0.062	0.989	12.5	20.5		5107

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	2.85	3			3.102	3.249	0.962	0.518		20.7

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7AHW	2.85	44.21	5071	258	99.49	0.188	0.1849	0.2369	81.095

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]
-1.738			-1.738		3.475

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.522
r_dihedral_angle_3_deg	21.104
r_dihedral_angle_4_deg	19.687
r_lrange_other	15.739
r_lrange_it	15.727
r_scangle_it	13.411
r_scangle_other	13.405
r_mcangle_other	8.876
r_mcangle_it	8.856
r_scbond_it	8.802
r_scbond_other	8.799
r_dihedral_angle_1_deg	8.498
r_mcbond_it	6.246
r_mcbond_other	6.194
r_angle_refined_deg	1.686
r_angle_other_deg	1.164
r_nbd_refined	0.202
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.153
r_nbd_other	0.15
r_xyhbond_nbd_refined	0.12
r_symmetry_nbd_refined	0.097
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.059
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1058
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	2

Software

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