Experiment: 1YXA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QLP	PDB ENTRY 1QLP DIFFERENCES TO ALA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	295	0.1M Na tartarate, 0.1M HEPES, 24% PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.34	α = 90
b = 92.62	β = 90
c = 118.26	γ = 90

Symmetry
Space Group	P 21 21 21

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 315	Bent conical Si-mirror (Rh coating)	2004-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C

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	2	100	92.4	0.075	15.59	3.2	62513	57467

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	2.07	72.9		0.415		2.1	4480

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1QLP DIFFERENCES TO ALA	2.1	30.01	54092	51453	2086	95.1	0.195	0.195	0.193	0.239	RANDOM	34.229

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]
-1.05			3.82		-2.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.273
r_dihedral_angle_4_deg	17.302
r_dihedral_angle_3_deg	14.725
r_scangle_it	5.995
r_dihedral_angle_1_deg	5.868
r_scbond_it	4.154
r_mcangle_it	2.656
r_mcbond_it	1.588
r_angle_refined_deg	1.224
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.273
r_dihedral_angle_4_deg	17.302
r_dihedral_angle_3_deg	14.725
r_scangle_it	5.995
r_dihedral_angle_1_deg	5.868
r_scbond_it	4.154
r_mcangle_it	2.656
r_mcbond_it	1.588
r_angle_refined_deg	1.224
r_nbtor_refined	0.307
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.165
r_symmetry_hbond_refined	0.144
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5723
Nucleic Acid Atoms
Solvent Atoms	396
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.