4Q2O | pdb_00004q2o

PDLIM4 PDZ in Complex with a Phage-Derived Peptide

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V1W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.6	292	25% PEG 4000, 0.1 M sodium acetate (pH 4.6), 0.1 M Sodium citrate tribasic, 0.2 M ammonium sulfate, VAPOR DIFFUSION, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.71	α = 90
b = 64.61	β = 93.05
c = 126.22	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	ADSC QUANTUM 210r		2007-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1		ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.1	50	99.3	0.04	0.036	26.1	4		31772

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	2.1	2.18	99.8		0.384		3.6	3156

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2v1w	2.1	20	31009	1565	97.73	0.2501	0.2478	0.25	0.292	0.3	RANDOM	73.699

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]
0.18		-0.16	0.52		-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.435
r_dihedral_angle_3_deg	17.529
r_dihedral_angle_4_deg	14.726
r_dihedral_angle_1_deg	6.603
r_scangle_it	4.962
r_mcangle_it	3.84
r_scbond_it	3.463
r_mcbond_it	2.593
r_angle_refined_deg	1.434
r_angle_other_deg	1.015
r_mcbond_other	0.296
r_symmetry_vdw_other	0.211
r_nbd_refined	0.208
r_nbd_other	0.186
r_nbtor_refined	0.17
r_symmetry_vdw_refined	0.155
r_xyhbond_nbd_refined	0.15
r_nbtor_other	0.087
r_chiral_restr	0.082
r_symmetry_hbond_refined	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3910
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms

Software

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