3VRL | pdb_00003vrl

Crystal structure of BMJ4 p24 capsid protein in complex with A10F9 Fab

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E6J	PDB ENTRY 1E6J (for FAB chains)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	PEG 3350, NaBr, NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.109	α = 90
b = 124.058	β = 90
c = 150.83	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	ADSC QUANTUM 315		2011-01-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9793	SSRF	BL17U

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	3.2	50	100	0.127		14	25000	24996	2	2

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	3.2	3.26	100		0.448

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRY 1E6J (for FAB chains)	3.2	37.02	25000	24996	1335	99.45	0.22	0.21484	0.21092	0.2075	0.29189	0.2846	RANDOM	69.991

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]
7.05			-1.12		-5.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.282
r_dihedral_angle_4_deg	22.725
r_dihedral_angle_3_deg	22.717
r_dihedral_angle_1_deg	8.677
r_scangle_it	2.122
r_angle_refined_deg	1.701
r_scbond_it	1.243
r_mcangle_it	0.984
r_mcbond_it	0.546
r_nbtor_refined	0.318
r_nbd_refined	0.264
r_symmetry_vdw_refined	0.215
r_xyhbond_nbd_refined	0.157
r_symmetry_hbond_refined	0.131
r_chiral_restr	0.112
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7806
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
MLPHARE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling