1ZMP | pdb_00001zmp

Crystal structure of human defensin-5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Experimental phases

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	HEPES, lithium sulfate monohydrate, dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.375	α = 90
b = 49.375	β = 90
c = 255.185	γ = 120

Symmetry
Space Group	P 65 2 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		2004-01-01	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	1.6	30	90.2	0.086	22.1	8.7	23239	23239

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	1.6	1.66	50		0.388	2.5	5.6

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	SAD	THROUGHOUT	Expermiental phases	1.65	19.73	20981	20981	1123	94.37	0.20046	0.19842	0.22	0.24027	RANDOM	18.213

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	0.02		0.03		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	11.736
r_dihedral_angle_1_deg	6.509
r_sphericity_bonded	3.367
r_scangle_it	2.764
r_mcangle_it	2.397
r_rigid_bond_restr	2.187
r_scbond_it	1.842
r_angle_refined_deg	1.643
r_mcbond_it	1.423
r_angle_other_deg	0.702
r_symmetry_vdw_other	0.537
r_nbd_other	0.433
r_symmetry_hbond_refined	0.317
r_symmetry_vdw_refined	0.313
r_xyhbond_nbd_refined	0.291
r_nbtor_other	0.258
r_nbd_refined	0.23
r_chiral_restr	0.116
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	924
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	55

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
SHELXD	phasing
SHARP	phasing