4BXR | pdb_00004bxr

Structure of the wild-type TCP10 domain of Danio rerio CPAP in complex with a peptide of Danio rerio STIL

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BXP	PDB ENTRY 4BXP (DISTORTED)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		100 MM TRIS PH 8.5, 200 MM CA ACETATE, 17% PEG-2000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.39	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.25	α = 90
b = 67.47	β = 113.92
c = 61.65	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	100	PIXEL	DECTRIS PIXEL		2012-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

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	2.2	56.4	99.9	0.1	7.6	4.8		23051		1.4

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	2.2	2.32	99.9		1.01	1.4	4.9

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 4BXP (DISTORTED)	2.2	51.13	21892	1145	99.83	0.23642	0.23427	0.24	0.27668	0.28	RANDOM	59.692

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]
1.66		-0.74	-2.75		1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.435
r_dihedral_angle_4_deg	18.937
r_dihedral_angle_3_deg	15.434
r_mcangle_it	7.864
r_dihedral_angle_1_deg	6.613
r_mcbond_it	5.311
r_angle_refined_deg	1.619
r_mcbond_other	1.418
r_angle_other_deg	1.149
r_xyhbond_nbd_other	0.261
r_nbd_refined	0.238
r_symmetry_vdw_other	0.225
r_symmetry_vdw_refined	0.219
r_symmetry_hbond_refined	0.215
r_nbd_other	0.207
r_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.182
r_nbtor_other	0.089
r_chiral_restr	0.084
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.004
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	3115
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing