5XCS | pdb_00005xcs

Crystal structure of 12CA5 Fv-clasp fragment with its antigen peptide

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HIL	1HIL, 5XCQ
experimental model	PDB	5XCQ	1HIL, 5XCQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.1M Na/K phosphate pH6.2, 1.4M (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.87	α = 90
b = 85.66	β = 125.71
c = 76.54	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	RAYONIX MX300HE		2015-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

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	2.2	42.83	98	0.14	13.6	7.5		24599

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	2.2	2.33	90.2		0.9	3.41	7.3

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	1HIL, 5XCQ	2.2	38.11	23282	1280	98.51	0.21005	0.20817	0.22	0.244	0.25	RANDOM	41.11

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]
-0.81		0.02	-3.8		2.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.33
r_dihedral_angle_4_deg	17.874
r_dihedral_angle_3_deg	14.319
r_dihedral_angle_1_deg	5.926
r_long_range_B_refined	4.101
r_long_range_B_other	3.653
r_scangle_other	1.863
r_mcangle_it	1.53
r_mcangle_other	1.53
r_angle_refined_deg	1.425
r_scbond_it	1.141
r_scbond_other	1.116
r_angle_other_deg	0.923
r_mcbond_it	0.912
r_mcbond_other	0.912
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2684
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing