8F0Y | pdb_00008f0y

Lipocalin-like Milk protein-1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	293	0.2M Potassium Nitrate, pH 6.9, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.672	α = 100.765
b = 33.038	β = 99.681
c = 38.64	γ = 103.599

Symmetry
Space Group	P 1

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		2022-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D

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	2.1	37.02	96.7	0.112	0.158	0.112	0.98	3.5	2.6		8498

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	2.1	2.16	95.4		0.62	0.877	0.62	0.483		2.6

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	4NYQ	2.1	37.012	8498	433	96.689	0.199	0.1962	0.21	0.2523	0.27	40.13

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]
-2.312	1.22	0.946	-0.371	2.202	0.257

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.61
r_dihedral_angle_6_deg	17.18
r_lrange_it	14.139
r_lrange_other	14.135
r_scangle_it	11.815
r_scangle_other	11.81
r_dihedral_angle_2_deg	11.601
r_dihedral_angle_1_deg	8.106
r_scbond_it	7.909
r_scbond_other	7.903
r_mcangle_it	6.674
r_mcangle_other	6.672
r_mcbond_other	4.786
r_mcbond_it	4.785
r_angle_refined_deg	2.597
r_angle_other_deg	0.862
r_symmetry_nbd_refined	0.272
r_nbd_other	0.252
r_nbd_refined	0.221
r_symmetry_nbd_other	0.216
r_nbtor_refined	0.204
r_xyhbond_nbd_refined	0.193
r_symmetry_xyhbond_nbd_refined	0.138
r_chiral_restr	0.124
r_symmetry_nbtor_other	0.102
r_symmetry_xyhbond_nbd_other	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.014
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1221
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms	42

Software

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