3M1B | pdb_00003m1b

Crystal structure of human FcRn with a dimeric peptide inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3M17	PDB ENTRY 3M17

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	294	2ul protein:peptide with 2ul buffer containing 100 mM phosphate/citric acid, 22% PEG 1000 and 8% ethanol , pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.05	α = 90
b = 158.431	β = 90.11
c = 82.539	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray					2009-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	3.1	50	90.4			29051	29051		-4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.2	58

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 3M17	3.1	37.24	27550	27550	1475	100	0.31803	0.31386	0.31	0.39658	0.4	RANDOM	106.575

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]
-1.44		-0.04	1.06		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.208
r_dihedral_angle_3_deg	21.204
r_dihedral_angle_4_deg	16.505
r_dihedral_angle_1_deg	6.484
r_angle_refined_deg	1.184
r_scangle_it	0.892
r_mcangle_it	0.788
r_scbond_it	0.548
r_mcbond_it	0.445
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.208
r_dihedral_angle_3_deg	21.204
r_dihedral_angle_4_deg	16.505
r_dihedral_angle_1_deg	6.484
r_angle_refined_deg	1.184
r_scangle_it	0.892
r_mcangle_it	0.788
r_scbond_it	0.548
r_mcbond_it	0.445
r_nbtor_refined	0.308
r_nbd_refined	0.227
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.184
r_symmetry_hbond_refined	0.154
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11241
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.