2PKT | pdb_00002pkt

Crystal structure of the human CLP-36 (PDLIM1) bound to the C-terminal peptide of human alpha-actinin-1

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		in-house model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	40% PEG 300, 0.2M Calcium acetate, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.74	α = 90
b = 38.74	β = 90
c = 246.46	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	MARMOSAIC 225 mm CCD		2007-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.79987	SLS	X10SA

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	1.5	50	98.3	0.114	14.3	13.8	18632	18632			18.3

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	1.5	1.59	89.6		0.55	2.8	6.6	2617

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	in-house model	1.5	41.06	18632	18632	960	98.84	0.213	0.213	0.212	0.22	0.231	0.24	RANDOM	7.375

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]
0.17	0.09		0.17		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.057
r_dihedral_angle_4_deg	9.39
r_dihedral_angle_3_deg	9.282
r_dihedral_angle_1_deg	5.118
r_scangle_it	1.082
r_angle_refined_deg	0.919
r_angle_other_deg	0.767
r_scbond_it	0.696
r_mcangle_it	0.39
r_mcbond_it	0.236
r_symmetry_vdw_other	0.213
r_nbd_refined	0.179
r_nbd_other	0.174
r_symmetry_vdw_refined	0.169
r_nbtor_refined	0.151
r_xyhbond_nbd_refined	0.107
r_metal_ion_refined	0.104
r_nbtor_other	0.074
r_symmetry_hbond_refined	0.073
r_chiral_restr	0.055
r_symmetry_metal_ion_refined	0.054
r_mcbond_other	0.048
r_bond_refined_d	0.005
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	677
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	26

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
XDS	data scaling