1ZMK

Crystal structure of human alpha-defensin-2 (variant Gly16-> D-ALA), P 42 21 2 space group

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	tri-sodium citrate dihydrate, Tris/HCl, PEG 8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.148	α = 90
b = 47.148	β = 90
c = 50.643	γ = 90

Symmetry
Space Group	P 42 21 2

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	0.9200	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	1.1	30	97.7	0.07	15.7	10.2	24405	24405

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	1.1	1.15	89.8		0.429	2.2	3.9

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Based on monomer of HNP-3 (PDB ID code 1DFN)	1.3	19.47	13688	734	98.76	0.16116	0.16116	0.16033	0.17676	RANDOM	15.779

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]
0.03			0.03		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.488
r_dihedral_angle_3_deg	10.723
r_dihedral_angle_4_deg	10.136
r_sphericity_free	9.842
r_dihedral_angle_1_deg	8.149
r_angle_other_deg	3.881
r_sphericity_bonded	3.526
r_scangle_it	3.38
r_mcangle_it	3.102
r_scbond_it	3.017
r_mcbond_it	2.553
r_angle_refined_deg	1.721
r_rigid_bond_restr	1.636
r_mcbond_other	1.012
r_symmetry_hbond_refined	0.424
r_symmetry_vdw_refined	0.306
r_nbd_refined	0.288
r_symmetry_vdw_other	0.279
r_xyhbond_nbd_other	0.258
r_xyhbond_nbd_refined	0.245
r_nbd_other	0.235
r_nbtor_refined	0.197
r_chiral_restr	0.183
r_nbtor_other	0.119
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	468
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	8

Software

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