2NLE | pdb_00002nle

Human beta-defensin-1 (Mutant Gln11Ala)

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, GLYCEROL, pH 4.6, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.22	α = 90
b = 22.78	β = 108.5
c = 40.15	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 300 mm CCD		2005-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	0.97180	APS	22-BM

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	1.35	40	99.7	0.037	29	3.9	13193	13193		-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)
	1.35	1.4	99.7		0.207	7.5	3.9	1284

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	1.35	30	13183	13183	926	99.72	0.154	0.154	0.151	0.15	0.198	RANDOM	15.479

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]
0.61		-0.08	-0.29		-0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.191
r_dihedral_angle_4_deg	13.165
r_dihedral_angle_3_deg	12.562
r_dihedral_angle_1_deg	6.423
r_scangle_it	4.868
r_scbond_it	4.196
RIGID-BOND RESTRAINTS (A**2)	3.552
r_mcangle_it	2.744
r_mcbond_it	2.051
r_angle_refined_deg	1.862
r_nbtor_refined	0.306
r_nbd_refined	0.234
r_symmetry_vdw_refined	0.212
r_symmetry_hbond_refined	0.156
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.139
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
SPHERICITY; FREE ATOMS (A**2)
SPHERICITY; BONDED ATOMS (A**2)

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	541
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	19

Software

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