3D9Y | pdb_00003d9y

Crystal Structure of Profilin from Schizosaccharomyces pombe

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	1.3 M Na Malonate; 0.2 M Hepes pH 7.0; 0.5% JeffamineED2001 [O O'-BIS (2-aminopropyl) polyethylene glycol 1900] from Hampton Research], VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.533	α = 90
b = 84.021	β = 93.73
c = 40.42	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	273	IMAGE PLATE	MAR scanner 345 mm plate		2006-10-02	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	MARRESEARCH		2007-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU 200	1.54178
2	SYNCHROTRON	NSLS BEAMLINE X29A	1.08090	NSLS	X29A

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	1.65	50	92	0.039	0.048	19.3	2.8	59358	24741

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	1.65	1.81	73.3		0.256	0.17	2.23	1.9	1783

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 (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 2ACG	1.65	42	24740	1262	84.86	0.177	0.177	0.175	0.23	0.206	0.25	RANDOM	15.225

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]
1.78		-0.85	-1.37		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.257
r_dihedral_angle_3_deg	16.026
r_dihedral_angle_4_deg	14.438
r_dihedral_angle_1_deg	5.045
r_scangle_it	2.127
r_scbond_it	1.515
r_angle_refined_deg	1.255
r_mcangle_it	0.856
r_angle_other_deg	0.816
r_mcbond_it	0.656
r_symmetry_hbond_refined	0.442
r_chiral_restr	0.252
r_nbd_refined	0.205
r_nbtor_refined	0.178
r_nbd_other	0.177
r_xyhbond_nbd_refined	0.166
r_mcbond_other	0.141
r_symmetry_vdw_refined	0.127
r_symmetry_vdw_other	0.085
r_nbtor_other	0.08
r_symmetry_hbond_other	0.057
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1866
Nucleic Acid Atoms
Solvent Atoms	265
Heterogen Atoms	12

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection