5NBI | pdb_00005nbi

Principles for computational design of antibodies

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QQ9	3QQ9, 4JFZ
experimental model	PDB	4JFZ	3QQ9, 4JFZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1M NH4CH3CO2 0.05M Mg(CH3CO2)2 0.05M Cacodylate pH=6.5 15% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.909	α = 90
b = 67.909	β = 90
c = 182.181	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	PIXEL	DECTRIS PILATUS3 S 6M		2014-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97242	ESRF	ID23-1

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	2.1	60.73	93	0.074	6.5	10.9		28196

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	2.1	2.21	85.9		0.59	1.3	10.7

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	3QQ9, 4JFZ	2.1	60.73	27279	1405	97.84	0.2199	0.21794	0.23	0.2578	0.27	RANDOM	54.799

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]
0.46	0.23		0.46		-1.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.132
r_dihedral_angle_4_deg	21.315
r_dihedral_angle_3_deg	13.997
r_dihedral_angle_1_deg	7.239
r_long_range_B_refined	6.405
r_long_range_B_other	6.404
r_scangle_other	4.571
r_mcangle_it	3.842
r_mcangle_other	3.841
r_scbond_it	2.97
r_scbond_other	2.969
r_mcbond_it	2.603
r_mcbond_other	2.6
r_angle_refined_deg	1.45
r_angle_other_deg	0.909
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3303
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALEPACK	data scaling
PHASER	phasing