9F5B | pdb_00009f5b

Identification of zinc ions in LMO4.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RUT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.25 M Sodium Malonate pH 7, 20 % v/w PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.816	α = 90
b = 61.816	β = 90
c = 93.396	γ = 120

Symmetry
Space Group	P 3 1 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS 12M		2023-05-25	M	SINGLE WAVELENGTH
2	1	x-ray	80	PIXEL	DECTRIS PILATUS 12M		2023-05-25	M	SINGLE WAVELENGTH
3	1	x-ray	80	PIXEL	DECTRIS PILATUS 12M		2023-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I23	1.2853	Diamond	I23
2	SYNCHROTRON	DIAMOND BEAMLINE I23	1.2874	Diamond	I23
3	SYNCHROTRON	DIAMOND BEAMLINE I23	1.3051	Diamond	I23

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.8	53.534	100	0.11	1	18.4	18.8		19257

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83			3.08	0.35	0.5

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	THROUGHOUT	1.8	53.534	19198	967	99.72	0.2	0.1983	0.2049	0.2335	0.2404	46.685

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]
-0.124	-0.062		-0.124		0.403

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.259
r_dihedral_angle_3_deg	13.119
r_lrange_it	10.091
r_scangle_it	8.48
r_dihedral_angle_1_deg	6.21
r_scbond_it	5.982
r_mcangle_it	5.707
r_mcbond_it	4.305
r_dihedral_angle_2_deg	3.868
r_angle_refined_deg	1.659
r_nbtor_refined	0.308
r_xyhbond_nbd_refined	0.2
r_nbd_refined	0.198
r_symmetry_nbd_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.136
r_metal_ion_refined	0.131
r_chiral_restr	0.096
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_ext_dist_refined_b

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1273
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing