3M0U | pdb_00003m0u

Crystal Structure of the R21D mutant of alpha-spectrin SH3 domain. Hexagonal crystal obtained in sodium formate at pH 6.5.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SHG	PDB entry 1SHG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	batch, under oil	6.5	298	2 M sodium formate, 0.1 M MES pH 6.5, batch, under oil, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.929	α = 90
b = 42.929	β = 90
c = 127.486	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	100	CCD	CCD ADSC_Q210		2008-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM16	0.97752	ESRF	BM16

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	1.1	37.19	95.1	0.073	0.073	12.8	4.3	29341	27903			10.78

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	1.1	1.14	81.9		0.094	0.094	7.1	2.3	2330

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 (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 1SHG	1.1	20	27739	26450	1412	95.35	0.15776	0.158	0.157	0.15	0.168	0.16	RANDOM	19.748

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]
-0.1	-0.05		-0.1		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	47.403
r_sphericity_free	22.595
r_dihedral_angle_4_deg	21.605
r_scangle_it	11.822
r_sphericity_bonded	10.812
r_dihedral_angle_3_deg	10.323
r_scbond_it	7.941
r_mcangle_it	6.051
r_dihedral_angle_1_deg	5.454
r_rigid_bond_restr	4.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	47.403
r_sphericity_free	22.595
r_dihedral_angle_4_deg	21.605
r_scangle_it	11.822
r_sphericity_bonded	10.812
r_dihedral_angle_3_deg	10.323
r_scbond_it	7.941
r_mcangle_it	6.051
r_dihedral_angle_1_deg	5.454
r_rigid_bond_restr	4.54
r_mcbond_it	3.978
r_angle_refined_deg	1.979
r_chiral_restr	0.151
r_bond_refined_d	0.022
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	473
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	3

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.