9W3Y | pdb_00009w3y

X-ray Crystal Structure of Pseudoazurin Met16Gly variant (Tris-HCl pH 7.6)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8WQZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	298	0.1 M Tris-HCl, 39% (w/v) PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.748	α = 90
b = 69.984	β = 90
c = 94.239	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	PIXEL	DECTRIS EIGER X 4M		2025-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.0070	Photon Factory	BL-1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.5	47.12	100	0.998	11.2	6.7		65079			5.985

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	100		0.661	2	6.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.5	47.12	65010	3261	99.935	0.143	0.1401	0.1388	0.198	0.1954	11.808

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]
-0.082			-0.112		0.194

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.312
r_lrange_it	14.067
r_dihedral_angle_2_deg	13.695
r_lrange_other	10.78
r_dihedral_angle_3_deg	10.465
r_dihedral_angle_1_deg	7.113
r_scangle_it	4.899
r_scangle_other	4.898
r_mcangle_other	4.046
r_mcangle_it	4.044
r_rigid_bond_restr	3.252
r_scbond_it	3.214
r_scbond_other	3.214
r_mcbond_it	2.567
r_mcbond_other	2.564
r_angle_refined_deg	1.611
r_angle_other_deg	0.552
r_symmetry_nbd_refined	0.274
r_nbd_other	0.219
r_nbd_refined	0.218
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.173
r_metal_ion_refined	0.157
r_xyhbond_nbd_refined	0.148
r_symmetry_xyhbond_nbd_refined	0.133
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.02
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3590
Nucleic Acid Atoms
Solvent Atoms	809
Heterogen Atoms	5

Software

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