7BXV | pdb_00007bxv

11A1 antibody-peptide complex

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PEG3,350, NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.639	α = 90
b = 123.774	β = 99.743
c = 45.692	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	100	PIXEL	DECTRIS PILATUS 2M		2018-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.0000	Photon Factory	AR-NE3A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.75	100	100	0.063	0.068	0.026	21.5	6.8		44761

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78			0.135	0.147	0.056

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1MNU	1.75	45.074	42474	2250	99.942	0.167	0.1655	0.17	0.1944	0.2	1	16.057

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]
0.091		0.2	-0.7		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.229
r_dihedral_angle_4_deg	22.378
r_dihedral_angle_3_deg	11.919
r_dihedral_angle_1_deg	8.133
r_lrange_it	5.253
r_lrange_other	5.252
r_scangle_it	3.577
r_scangle_other	3.576
r_mcangle_other	2.499
r_mcangle_it	2.497
r_scbond_it	2.423
r_scbond_other	2.422
r_mcbond_it	1.672
r_mcbond_other	1.663
r_angle_other_deg	1.451
r_angle_refined_deg	1.275
r_nbd_other	0.286
r_symmetry_nbd_other	0.214
r_symmetry_nbd_refined	0.199
r_nbd_refined	0.192
r_symmetry_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.135
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.057
r_gen_planes_refined	0.014
r_gen_planes_other	0.005
r_bond_refined_d	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3365
Nucleic Acid Atoms
Solvent Atoms	431
Heterogen Atoms	20

Software

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