5I18 | pdb_00005i18

CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV1-69/IGKV4-1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DD8	2DD8,1LVE
experimental model	PDB	1LVE	2DD8,1LVE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	10% PEG 8K, 8% ETHYLENE GLYCOL, 0.1 M HEPES PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.39	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.04	α = 90
b = 120.04	β = 90
c = 64.17	γ = 90

Symmetry
Space Group	P 4 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	95	CCD	RIGAKU SATURN 944	VARIMAX HF	2008-09-15	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	1.92	30	98.5	0.093	29.2	22.3		35965		-3	19.6

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	1.92	1.97	82.8		0.231	8.1	8.8

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	2DD8,1LVE	1.92	15	34850	1025	95.6	0.16839	0.16706	0.17	0.2132	0.22	RANDOM	20

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]
0.07			0.07		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.768
r_dihedral_angle_4_deg	21.983
r_scangle_it	20.2
r_scbond_it	19.502
r_dihedral_angle_3_deg	11.882
r_dihedral_angle_1_deg	6.131
r_mcangle_it	3.944
r_mcbond_it	2.327
r_angle_refined_deg	1.115
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_refined
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3263
Nucleic Acid Atoms
Solvent Atoms	399
Heterogen Atoms	24

Software

Software
Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
REFMAC	refinement