1U5X | pdb_00001u5x

Crystal structure of murine APRIL at pH 5.0

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U5Z	APRIL at pH 8.5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	292	0.1 M Citric Acid, 1.0 M LiCL, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.1	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.779	α = 90
b = 90.779	β = 90
c = 90.779	γ = 90

Symmetry
Space Group	I 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH	osmic mirrors	2004-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.8	30	100	0.042	30.8	8.5	11701	11701		-3	30

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	1.8	1.86	100		0.442	5	5.5	1162

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	APRIL at pH 8.5	1.8	30	11701	11697	1136	99.97	0.2179	0.21799	0.21375	0.21	0.2563	0.25	RANDOM	19.636

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.584
r_dihedral_angle_4_deg	24.941
r_dihedral_angle_3_deg	15.216
r_dihedral_angle_1_deg	6.739
r_scangle_it	5.559
r_scbond_it	3.852
r_mcangle_it	3.604
r_mcbond_it	2.57
r_angle_refined_deg	1.511
r_angle_other_deg	0.828
r_symmetry_vdw_other	0.302
r_nbd_other	0.257
r_symmetry_vdw_refined	0.231
r_symmetry_hbond_refined	0.211
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.091
r_nbtor_other	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_gen_planes_other	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	994
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing