3TRY | pdb_00003try

Crystal structure of racemic villin headpiece subdomain in space group I-4c2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YRF	PDB ENTRY 1YRF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.75	298	2.0 M ammonium sulfate, 6% isopropanol, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.128	α = 90
b = 63.128	β = 90
c = 39.135	γ = 90

Symmetry
Space Group	I -4 c 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CCD	BRUKER SMART 6000		2011-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	22.319	97.1	0.1259	16.39	17.58	1824	1772

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.36	100		0.3122	8.58	16.21

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1YRF	2.3	22.319	1824	1694	79	97.04	0.20186	0.20047	0.2	0.23006	0.23	RANDOM	20.909

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]
-0.04			-0.04		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.075
r_dihedral_angle_4_deg	11.171
r_dihedral_angle_1_deg	3.718
r_scangle_it	2.472
r_angle_refined_deg	1.75
r_scbond_it	1.385
r_mcangle_it	0.851
r_mcbond_it	0.412
r_chiral_restr	0.107
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_3_deg
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	277
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	5

Software

Software
Software Name	Purpose
SAINT	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction
SAINT	data scaling
PHASER	phasing