2GSI | pdb_00002gsi

Crystal Structure of a Murine Fab in Complex with an 11 Residue Peptide Derived from Staphylococcal Nuclease

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F11	PDB entries: 1f11, 2aju, 1f58, 1cr9
experimental model	PDB	2AJU	PDB entries: 1f11, 2aju, 1f58, 1cr9
experimental model	PDB	1F58	PDB entries: 1f11, 2aju, 1f58, 1cr9
experimental model	PDB	1CR9	PDB entries: 1f11, 2aju, 1f58, 1cr9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	291	18% PEG 2000, 16% isopropanol, 0.1 M sodium citrate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.739	α = 90
b = 131.04	β = 90
c = 291.34	γ = 90

Symmetry
Space Group	C 2 2 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	Pt coated toroidal Si mirror	2004-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1000	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.8	50	84.6	0.12	0.12	24.1	4.4	42035	42035		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	83.6		0.489	0.489	4.9	4.8

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entries: 1f11, 2aju, 1f58, 1cr9	2.81	48.74	41984	39809	2175	84.25	0.22451	0.22074	0.29278	RANDOM	37.415

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]
0.24			-0.45		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.303
r_dihedral_angle_3_deg	20.904
r_dihedral_angle_4_deg	20.022
r_dihedral_angle_1_deg	8.095
r_scangle_it	2.641
r_scbond_it	1.616
r_angle_refined_deg	1.394
r_mcangle_it	1.136
r_mcbond_it	0.646
r_symmetry_vdw_refined	0.338
r_nbtor_refined	0.317
r_symmetry_hbond_refined	0.259
r_nbd_refined	0.257
r_xyhbond_nbd_refined	0.165
r_chiral_restr	0.096
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13309
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing