3K48 | pdb_00003k48

Crystal structure of APRIL bound to a peptide

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XU1	Chain A from pdb 1xu1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	2ul drops of protein (5 mg/mg. at pH 9.7) was added to 2 uL of 4M formate. Crystals formed immediately, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.811	α = 90
b = 84.771	β = 99.45
c = 55.562	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	ADSC QUANTUM 210		2005-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	1.0	ALS	5.0.1

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	2.8	50	99.6	0.108	12.4	3.7	11453	11453		-3	50

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	2.8	2.9	98.4		0.506	2.5	3.6	1126

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	Chain A from pdb 1xu1	2.8	30	10257	1143	99.59	0.21169	0.20548	0.21	0.2669	0.27	thin shells	16.768

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]
-0.37		-1.52	-2.51		2.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.822
r_dihedral_angle_4_deg	17.592
r_dihedral_angle_3_deg	15.047
r_dihedral_angle_1_deg	6.842
r_mcangle_it	2.929
r_scangle_it	2.872
r_mcbond_it	2.345
r_scbond_it	1.788
r_angle_refined_deg	1.252
r_angle_other_deg	0.953
r_mcbond_other	0.494
r_symmetry_vdw_other	0.294
r_symmetry_vdw_refined	0.237
r_nbd_other	0.198
r_nbd_refined	0.197
r_symmetry_hbond_refined	0.181
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.079
r_nbtor_other	0.079
r_bond_refined_d	0.01
r_bond_other_d	0.004
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3613
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
Blu-Ice	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling