2VWF | pdb_00002vwf

Grb2 SH3C (2)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VVK	PDB ENTRY 2VVK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		2M TRI-AMMONIUM CITRATE, 0.1M BIS-TRIS PROPANE PH7, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
1.58	22.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.166	α = 90
b = 41.166	β = 90
c = 107.915	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	CCD	MARMOSAIC 225 mm CCD	MIRRORS	2007-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	1.58	50	99.9	0.01	26.7	19.5		8066		1

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	1.58	1.64	100		1	2.3	19.3

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 ENTRY 2VVK	1.58	35.65	7645	369	99.99	0.18951	0.18812	0.2	0.21907	0.23	RANDOM	13.39

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]
0.54	0.27		0.54		-0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.739
r_dihedral_angle_1_deg	17.584
r_dihedral_angle_4_deg	13.963
r_dihedral_angle_3_deg	13.171
r_scangle_it	3.361
r_scbond_it	2.361
r_angle_refined_deg	1.597
r_mcangle_it	1.531
r_mcbond_it	1.294
r_angle_other_deg	0.967
r_symmetry_vdw_other	0.268
r_symmetry_vdw_refined	0.255
r_nbd_other	0.211
r_nbd_refined	0.198
r_nbtor_refined	0.189
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.096
r_nbtor_other	0.092
r_symmetry_hbond_refined	0.082
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.007
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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	570
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms

Software

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