4O4Y | pdb_00004o4y

Crystal structure of the anti-hinge rabbit antibody 2095-2 in complex with IDES hinge peptide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4MA3	PDB ENTRY 4MA3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1 M Tris, pH 8.5, 18.33% PEG3350, 0.2 M lithium sulfate, 5% isopropanol, cryoprotection: mother liquor + 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.41	α = 90
b = 89.37	β = 90
c = 83.39	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RIGAKU SATURN 944	VARIMAX HF	2009-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.85	25	89.2	0.059	17.5	8.9		37290		-3	29

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	1.85	1.92	51.6		0.242	6.1	6.9

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	PDB ENTRY 4MA3	1.85	25	35290	1875	88.96	0.1942	0.1919	0.21	0.2367	0.25	RANDOM	33.146

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]
0.09			0.66		-0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.412
r_dihedral_angle_4_deg	13.56
r_dihedral_angle_3_deg	12.914
r_dihedral_angle_1_deg	6.283
r_scangle_it	2.689
r_scbond_it	1.701
r_angle_refined_deg	1.368
r_mcangle_it	1.162
r_angle_other_deg	0.842
r_mcbond_it	0.666

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.412
r_dihedral_angle_4_deg	13.56
r_dihedral_angle_3_deg	12.914
r_dihedral_angle_1_deg	6.283
r_scangle_it	2.689
r_scbond_it	1.701
r_angle_refined_deg	1.368
r_mcangle_it	1.162
r_angle_other_deg	0.842
r_mcbond_it	0.666
r_mcbond_other	0.183
r_chiral_restr	0.082
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3291
Nucleic Acid Atoms
Solvent Atoms	492
Heterogen Atoms	30

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	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.