2NLD | pdb_00002nld

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
1.93	36.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.84	α = 90
b = 23.57	β = 107
c = 40.45	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	IMAGE PLATE	MAR scanner 345 mm plate	Osmic mirrors	2005-07-21	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	1.49	50	92.8	0.055	26	5.1	9213	9213		-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)
	1.49	1.54	77.2		0.266	4.5	3.5	741

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	1.49	30	9202	9202	652	93.17	0.138	0.138	0.134	0.13	0.199	RANDOM	14.28

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]
-0.19		-0.63	-0.05		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.945
r_dihedral_angle_4_deg	22.935
r_dihedral_angle_3_deg	9.715
r_dihedral_angle_1_deg	5.983
r_scangle_it	3.14
r_mcangle_it	2.782
r_scbond_it	2.279
r_mcbond_it	2.179
RIGID-BOND RESTRAINTS (A**2)	1.829
r_angle_refined_deg	1.569
r_nbtor_refined	0.321
r_nbd_refined	0.283
r_symmetry_hbond_refined	0.21
r_xyhbond_nbd_refined	0.198
r_symmetry_vdw_refined	0.177
r_chiral_restr	0.147
r_bond_refined_d	0.017
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	538
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	14

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