3K74 | pdb_00003k74

Disruption of protein dynamics by an allosteric effector antibody

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HCV	PDB entries 1HCV, 5DFR
experimental model	PDB	5DFR	PDB entries 1HCV, 5DFR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	298	40% v/v PEG300, 5% w/v PEG1000, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.3	α = 90
b = 62.322	β = 90
c = 102.848	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 210		2008-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.98	SOLEIL	PROXIMA 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	1.9	30	99.9	0.102	12.5	7.1		28725

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	1.9	1.93	100		0.388		7.2	1394

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	PDB entries 1HCV, 5DFR	1.95	7.99	26145	1333	99.98	0.198	0.196	0.2103	0.24	0.2476	RANDOM	33.372

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]
0.01			0.43		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.812
r_dihedral_angle_4_deg	22.897
r_dihedral_angle_3_deg	14.812
r_dihedral_angle_1_deg	7.689
r_scangle_it	5.043
r_scbond_it	3.218
r_mcangle_it	2.035
r_angle_refined_deg	1.746
r_mcbond_it	1.313
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.273
r_symmetry_hbond_refined	0.249
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.205
r_chiral_restr	0.12
r_bond_refined_d	0.018
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2149
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
PHASER	phasing