5MHH | pdb_00005mhh

Crystal structure of engineered human lipocalin 2 carrying p-boronophenylalanine at position 36

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I0A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	2.4 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.857	α = 90
b = 90.857	β = 90
c = 44.2	γ = 90

Symmetry
Space Group	I 4

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		2015-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91801	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.888	64.246	99.9	0.131	0.141	0.052	8.7	7.3	12330	12330

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	99.5		0.341	2	7.3

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3I0A	2	64.246	11723	605	99.83	0.1836	0.181	0.19	0.2326	0.24	RANDOM	34.564

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]
0.63			0.63		-1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.416
r_dihedral_angle_3_deg	12.906
r_dihedral_angle_4_deg	8.365
r_mcangle_it	7.286
r_dihedral_angle_1_deg	6.635
r_mcbond_it	6.189
r_mcbond_other	6.011
r_angle_refined_deg	1.39
r_angle_other_deg	0.908
r_chiral_restr	0.086

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.416
r_dihedral_angle_3_deg	12.906
r_dihedral_angle_4_deg	8.365
r_mcangle_it	7.286
r_dihedral_angle_1_deg	6.635
r_mcbond_it	6.189
r_mcbond_other	6.011
r_angle_refined_deg	1.39
r_angle_other_deg	0.908
r_chiral_restr	0.086
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1499
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	15

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.