6V4R | pdb_00006v4r

Crystal structure of a chimeric MR78-like antibody chimera-1 Fab

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JRP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	287	4.5 M NaCl, 0.1 M HEPES, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
5	75.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.78	α = 90
b = 133.78	β = 90
c = 91.91	γ = 120

Symmetry
Space Group	P 31 2 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	CCD	MARMOSAIC 300 mm CCD		2018-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.48	57.93	99.2	0.342	0.084	8.8	16.6		12393			145.12

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.48	3.54	98.7		4.159	0.995	1.1	17.3

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5JRP	3.48	57.93	11852	524	99.01	0.2961	0.2946	0.3273	RANDOM	172.603

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]
6.54	3.27		6.54		-21.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.546
r_mcangle_it	19.239
r_mcbond_other	14.163
r_mcbond_it	14.156
r_dihedral_angle_4_deg	13.47
r_dihedral_angle_3_deg	7.527
r_dihedral_angle_1_deg	4.18
r_angle_other_deg	2.433
r_angle_refined_deg	2.178
r_chiral_restr	0.115

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.546
r_mcangle_it	19.239
r_mcbond_other	14.163
r_mcbond_it	14.156
r_dihedral_angle_4_deg	13.47
r_dihedral_angle_3_deg	7.527
r_dihedral_angle_1_deg	4.18
r_angle_other_deg	2.433
r_angle_refined_deg	2.178
r_chiral_restr	0.115
r_bond_other_d	0.036
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
r_gen_planes_other	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3259
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
xia2	data reduction
PHENIX	refinement

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.