6V4Q | pdb_00006v4q

Crystal structure of a MR78-like antibody naive-1 Fab

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1W72

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	1% w/v PEG 8000, 20% v/v 2-Propanol, 0.1 M Tris, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.98	α = 90
b = 73.12	β = 90
c = 105.16	γ = 90

Symmetry
Space Group	P 21 21 21

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		2018-06-20	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	1.39	43.78	99.4	0.058	0.025	16	5		99126			11.256

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	1.39	1.41	92		0.4	0.245	2.4	2.3

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1W72	1.39	43.78	94164	4880	99.31	0.1658	0.1647	0.1872	0.2109	RANDOM	15.089

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]
-0.16			-0.16		0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.403
r_dihedral_angle_4_deg	17.638
r_dihedral_angle_3_deg	12.391
r_dihedral_angle_1_deg	7.459
r_angle_other_deg	2.432
r_mcangle_it	2.29
r_angle_refined_deg	1.953
r_mcbond_it	1.511
r_mcbond_other	1.504
r_chiral_restr	0.103
r_bond_other_d	0.036
r_bond_refined_d	0.016
r_gen_planes_other	0.014
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3304
Nucleic Acid Atoms
Solvent Atoms	504
Heterogen Atoms	34

Software

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