1ZMI | pdb_00001zmi

Crystal structure of human alpha_defensin-2 (variant GLY16->D-ALA), P 32 2 1 space group )

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DFN	Based on monomer of HNP-3 (PDB code 1DFN)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	lithium sulfate, PEG8000, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3	58.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.685	α = 90
b = 71.685	β = 90
c = 54.882	γ = 120

Symmetry
Space Group	P 32 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	MARRESEARCH		2004-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.000	APS	22-BM

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	1.15	30	98.5	0.09	17	8.4	57187	57187

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	1.15	1.22	90.4		0.513	2.4	4.4

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Based on monomer of HNP-3 (PDB code 1DFN)	1.15	12	54227	54227	2891	98.53	0.16876	0.16807	0.2	0.18202	RANDOM	14.858

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]
-0.16	-0.08		-0.16		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.987
r_dihedral_angle_4_deg	15.648
r_dihedral_angle_3_deg	12.241
r_sphericity_free	9.57
r_dihedral_angle_1_deg	8.025
r_scangle_it	3.785
r_sphericity_bonded	3.721
r_scbond_it	3.02
r_mcangle_it	2.887
r_mcbond_it	2.198
r_angle_refined_deg	1.89
r_angle_other_deg	1.84
r_rigid_bond_restr	1.659
r_mcbond_other	1.116
r_chiral_restr	0.413
r_symmetry_vdw_refined	0.3
r_symmetry_vdw_other	0.285
r_nbd_other	0.239
r_xyhbond_nbd_refined	0.223
r_nbtor_refined	0.201
r_nbd_refined	0.197
r_symmetry_hbond_refined	0.194
r_nbtor_other	0.089
r_xyhbond_nbd_other	0.06
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	936
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing