2NLF | pdb_00002nlf

Human beta-defensin-1 (Mutant Leu13Glu)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IJV	PDB entry 1IJV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.6	293	PEG 4000, AMMONIUM SULFATE, SODIUM ACETATE, pH 4.6, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.01	α = 90
b = 46.79	β = 97.3
c = 28.56	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	IMAGE PLATE	MAR scanner 345 mm plate	osmic mirrors	2004-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.45	40	99	0.07	18	4.5	13851	13851		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.45	1.5	97.2		0.189	5.8	3.6	1365

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1IJV	1.45	30	13844	13844	988	98.96	0.143	0.143	0.14	0.14	0.184	RANDOM	13.457

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		0.01	-0.11		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.743
r_dihedral_angle_4_deg	32.131
r_dihedral_angle_3_deg	10.307
r_dihedral_angle_1_deg	6.25
r_scangle_it	4.424
r_scbond_it	3.427
r_mcangle_it	2.512
RIGID-BOND RESTRAINTS (A**2)	1.987
r_mcbond_it	1.871
r_angle_refined_deg	1.672
r_nbtor_refined	0.302
r_nbd_refined	0.25
r_symmetry_vdw_refined	0.203
r_xyhbond_nbd_refined	0.163
r_symmetry_hbond_refined	0.155
r_chiral_restr	0.113
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
SPHERICITY; FREE ATOMS (A**2)
SPHERICITY; BONDED ATOMS (A**2)

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	574
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	20

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing